Human-mediated Gene Flow Research Articles

Chinese Populations of Magnaporthe oryzae Serving as a Source of Human-Mediated Gene Flow to Asian Countries: A Population Genomic Analysis

Magnaporthe oryzae, a filamentous heterothallic ascomycete fungus that serves as the causative agent of rice blast disease, is globally distributed in rice-growing regions. Populations shaped by environmental factors and human intervention play important roles in the formation of genetic structure. In this study, population structures and spatiotemporal dynamics were investigated based on large-scale whole genomic sequences of rice-infecting M. oryzae around the world. By analyzing these genetic structures, we identified divergent clades that crossed geographic boundaries. While we observed associations between the isolates and their geographic origins, we also found that there were frequent migration events occurring across Asia in main rice cultivation regions. Within Asia, China was the migration origin, facilitating gene flows to Japan and South Korea. Since the 1970s, the genetic diversity of M. oryzae populations in China has also shown a steadily increasing trend, continuing through to the 2020s. Additionally, our analysis of the evolutionary history of Asian M. oryzae populations provided insights into the population expansion that has taken place in recent decades. Overall, our findings indicate that human-mediated gene flows played a pivotal role in shaping the genetic structure of M. oryzae.

Genetic diversity and historical demography of underutilised goat breeds in North-Western Europe

In the last decade, several studies aimed at dissecting the genetic architecture of local small ruminant breeds to discover which variations are involved in the process of adaptation to environmental conditions, a topic that has acquired priority due to climate change. Considering that traditional breeds are a reservoir of such important genetic variation, improving the current knowledge about their genetic diversity and origin is the first step forward in designing sound conservation guidelines. The genetic composition of North-Western European archetypical goat breeds is still poorly exploited. In this study we aimed to fill this gap investigating goat breeds across Ireland and Scandinavia, including also some other potential continental sources of introgression. The PCA and Admixture analyses suggest a well-defined cluster that includes Norwegian and Swedish breeds, while the crossbred Danish landrace is far apart, and there appears to be a close relationship between the Irish and Saanen goats. In addition, both graph representation of historical relationships among populations and f4-ratio statistics suggest a certain degree of gene flow between the Norse and Atlantic landraces. Furthermore, we identify signs of ancient admixture events of Scandinavian origin in the Irish and in the Icelandic goats. The time when these migrations, and consequently the introgression, of Scandinavian-like alleles occurred, can be traced back to the Viking colonisation of these two isles during the Viking Age (793-1066 CE). The demographic analysis indicates a complicated history of these traditional breeds with signatures of bottleneck, inbreeding and crossbreeding with the improved breeds. Despite these recent demographic changes and the historical genetic background shaped by centuries of human-mediated gene flow, most of them maintained their genetic identity, becoming an irreplaceable genetic resource as well as a cultural heritage.

SSRs MARKERS REVEAL HIGH GENETIC DIVERSITY AND LIMITED DIFFERENTIATION AMONG POPULATIONS OF NATIVE GUATEMALAN AVOCADO

Even though Guatemala is considered one of the three domestication centres of the avocado (Persea americana Mill), little is known about the genetic diversity of its native populations. This is the first study to explore avocado genetic diversity and population structure in native dispersal areas using microsatellite markers. We sampled 189 avocado trees grown from seeds in eight geographical populations, and 12 microsatellite loci were tested for diversity. There were a total of 289 alleles found throughout the 12 loci, with an average of 23.83 alleles per locus. The average observed and expected heterozygosity were 0.53 and 0.83, respectively. The analysis of molecular variance revealed that the eight populations comprised around 2% of the variation. Five of the 28 G'ST(Nei) pairwise comparisons indicated no genetic difference. We discovered a mixture of avocado trees from various populations using unweighted pair group method with arithmetic mean (UPGMA) hierarchical cluster analysis. The sampled individuals were classified into three main genetic clusters by the model-based STRUCTURE and discriminant analysis of principal components (DAPC). The weak genetic structure exhibited by mixing avocado trees from different populations could be mainly attributed to high human-mediated gene flow (Nm = 12.25) due to avocado's importance in food, culture, and Guatemala's religion. The high genetic diversity found in the avocado germplasm suggests that it might be a valuable source of variable alleles that could be used in breeding programs for this crop in Guatemala.

Population genomics of selectively neutral genetic structure and herbicide resistance in UK populations of Alopecurus myosuroides.

Alopecurus myosuroides (blackgrass) is a major weed in Europe with known resistance to multiple herbicide modes of action. In the UK, there is evidence that blackgrass has undergone a range expansion. In this paper, genotyping-by-sequencing and population-level herbicide resistance phenotypes are used to explore spatial patterns of selectively neutral genetic variation and resistance. We also perform a preliminary genome-wide association study (GWAS) and genomic prediction analysis to evaluate the potential of these approaches for investigating nontarget site herbicide resistance. Blackgrass was collected from 47 fields across the British Isles and up to eight plants per field population (n = 369) were genotyped by Restriction site-associated DNA (RAD)-sequencing. A total of 20 426 polymorphic loci were identified and used for population genetic analyses. Phenotypic assays revealed significant variation in herbicide resistance between populations. Population structure was weak (FST = 0.024-0.048), but spatial patterns were consistent with an ongoing westward and northward range expansion. We detected strong and consistent Wahlund effects (FIS = 0.30). There were no spatial patterns of herbicide resistance or evidence for confounding with population structure. Using a combination of population-level GWAS and genomic prediction we found that the top 20, 200, and 2000 GWAS loci had higher predictive abilities for fenoxaprop resistance compared to all markers. There is likely extensive human-mediated gene flow between field populations of the weed blackgrass at a national scale. The lack of confounding of adaptive and neutral genetic variation can enable future, more extensive GWAS analyses to identify the genetic architecture of evolved herbicide resistance. © 2020 Society of Chemical Industry.

Deciphering Anthropogenic Effects on the Genetic Background of the Red Deer in the Iberian Peninsula

Anthropogenic hybridization is one of the greatest threats to global biodiversity. It incites human-mediated gene flow between non-native/exotic and native taxa, which can have irreversible effects on native species or locally adapted populations, eventually leading to extinction. The red deer, Cervus elaphus, is a game species that, due to its extraordinary economic value, has been introduced in several regions throughout Europe. However, the consequences of those introductions on native populations, namely on their genetic background, have been poorly addressed. This study is focused on the Iberian Peninsula and aims to: i) assess the extent of anthropogenic hybridization/introgression of introduced red deer into the native Iberian populations; ii) evaluate the impact of red deer management regimes on the observed hybridization/introgression patterns; and iii) assess how hybridization/introgression influence the current genetic diversity of native Iberian populations. A set of 11 microsatellites and a 329 bases pair fragment of the mitochondrial D-loop gene were used to estimate nuclear admixture and mitochondrial introgression in 1132 individuals sampled across 46 red deer populations throughout Iberia. A Bayesian approach implemented in the STRUCTURE program was employed to investigate the proportion of admixture between native populations and non-native red deer. Results showed that 17% of individuals presented signs of non-native recent ancestors and 10.1% had non-native mitochondrial haplotypes, reaching an overall hybridization/introgression rate of 23%. Non-native or hybrid individuals were found throughout 40 Iberian red deer populations, and the percentages per population varied between 3.3% and 75.0%, independently of the management regime. Mitochondrial introgression was observed across 15 Iberian red deer populations, being more frequent in free-ranging individuals (16.2%) than in fenced populations (9.2%) but was completely absent from public-owned populations. Nuclear genetic diversity correlated positively with the proportion of hybrid individuals in public-owned populations. The genetic footprint of historical and current human-mediated translocations of non-native red deer into the Iberian Peninsula is evidenced in this study, highlighting the need to implement effective measures to avoid such practices both in Portugal and Spain, in order to preserve the endogenous genetic patrimony of the Iberian red deer populations.

Genomic and Fitness Consequences of Genetic Rescue in Wild Populations

Gene flow is an enigmatic evolutionary force because it can limit adaptation but may also rescue small populations from inbreeding depression [1-3]. Several iconic examples of genetic rescue-increased population growth caused by gene flow [4, 5]-have reversed population declines [6, 7]. However, concerns about outbreeding depression and maladaptive gene flow limit the use of human-mediated gene flow in conservation [8, 9]. Rescue effects of immigration through demographic and/or genetic mechanisms have received theoretical and empirical support, but studies that monitor initial and long-term effects of gene flow on individuals and populations in the wild are lacking. Here, we used individual-based mark-recapture, multigenerational pedigrees, and genomics to test the demographic and evolutionary consequences of manipulating gene flow in two isolated, wild Trinidadian guppy populations. Recipient and source populations originated from environments with different predation, flow, and resource regimes [10]. We documented 10-fold increases in population size following gene flow and found that, on average, hybrids lived longer and reproduced more than residents and immigrants. Despite overall genomic homogenization, alleles potentially associated with local adaptation were not entirely swamped by gene flow. Our results suggest that genetic rescue was caused not just by increasing individual genetic diversity, rather new genomic variation from immigrants combined with alleles from the recipient population resulted in highly fit hybrids and subsequent increases in population size. Contrary to the classic view of maladaptive gene flow, our study reveals conditions under which immigration can produce long-term fitness benefits in small populations without entirely swamping adaptive variation.

Human-Mediated Gene Flow Contributes to Metapopulation Genetic Structure of the Pathogenic Fungus Alternaria alternata from Potato.

Metapopulation structure generated by recurrent extinctions and recolonizations plays an important role in the evolution of species but is rarely considered in agricultural systems. In this study, generation and mechanism of metapopulation structure were investigated by microsatellite assaying 725 isolates of Alternaria alternata sampled from potato hosts at 16 locations across China. We found a single major cluster, no isolate-geography associations and no bottlenecks in the A. alternata isolates, suggesting a metapopulation genetic structure of the pathogen. We also found weak isolation-by-distance, lower among than within cropping region population differentiation, concordant moving directions of potato products and net gene flow and the highest gene diversity in the region with the most potato imports. These results indicate that in addition to natural dispersal, human-mediated gene flow also contributes to the generation and dynamics of the metapopulation genetic structure of A. alternata in China. Metapopulation structure increases the adaptive capacity of the plant pathogen as a result of enhanced genetic variation and reduced population fragmentation. Consequently, rigid quarantine regulations may be required to reduce population connectivity and the evolutionary potential of A. alternata and other pathogens with a similar population dynamics for a sustainable plant disease management.

The extent of historic translocation of Norway spruce forest reproductive material in Europe

Norway spruce seed has been traded extensively for at least three centuries throughout the natural distribution range in Europe and beyond. However, our knowledge about these transfers is limited. Historic data are essential tools to trace back human-mediated gene flow and for interpretation of recent genetic studies. Human-mediated gene flow can potentially have a major impact on the genetic composition of forest tree populations, yet our knowledge about seed sources used within the current species’ range is still limited. Norway spruce is one of the most important coniferous species in European forestry, and data drawing conclusions about the genetic composition of current populations are vital with regard to gene conservation and sustainable forest management. Because molecular data are not available on a more detailed scale, historic records provide crucial information about translocations. Our aim is to provide the first pan-European review on Norway spruce translocations from the seventeenth until the twentieth century. We analysed historic and recent literature compiling information on the cultivation and transfer of Norway spruce reproductive material. Historic records are compared with recent molecular studies. Seed exchanges have profoundly altered the native genetic population structure of Norway spruce. Especially, Central European seeds have been used throughout and beyond the natural distribution area. Figures illustrating the historic plantings in Europe are provided. Recent molecular data reveal persisting effects of past translocations. Historical records can be extremely useful for providing information about autochthony and thus guide gene conservation strategies and explain the performance of extant populations.

Natural genetic differentiation and human-mediated gene flow: the spatiotemporal tendency observed in a long-lived Cinnamomum camphora (Lauraceae) tree

The camphor tree (Cinnamomum camphora) is an important natural resource in East Asia. From the early eighteenth to mid-twentieth century, C. camphora was widely cultivated to obtain camphor, a white crystalline substance used as a repellent, a component of medicine, and an ingredient in the production of smokeless gunpowder and celluloid. The vast utilization and cultivation of C. camphora have obscured its natural distribution, and the genetic structure of this species was likely affected by both natural factors and human activities in different areas and at different times. To estimate this process, we collected 817 samples from Japan, China, and Taiwan, including samples from trees estimated to be hundreds to thousands of years old. Population genetic analyses using 11 microsatellite markers detected the footprints of ancient genetic differentiation and recent human-mediated gene flow. The strong genetic differentiation between areas (Japan vs. China and Taiwan) and the decreased genetic diversity in Japan can be ascribed to the long-term geographical isolation during and after the glacial period. Within each area, the genetic composition of the cultivated or planted populations was often inconsistent with the surrounding natural and/or older specimens. This finding may be due to the regional transfer of plant materials with no regard to their genetic origin. We also detected rare but evident immigration from different areas; furthermore, these non-native genets seemed to locally hybridize with the native genets. We suggest that the intentional transfer and/or artificial hybridization between areas should be prohibited in order to preserve the genetic composition of C. camphora.

Genetic analysis of Phytophthora sojae populations in Fujian, China

Phytophthora sojae is a destructive soilborne pathogen causing seedling damping‐off and root rot of soybean (Glycine max). The goal of this study was to determine the genetic structure of P. sojae populations in Fujian, China. Nine microsatellite markers were used to investigate the genetic variation in 19 P. sojae populations, sampled from Fujian Province and northeastern China (Jilin and Heilongjiang Provinces) between 2002 and 2013. Overall, a low genetic diversity, Hardy–Weinberg disequilibrium, and an index (an index of association) that was significantly different from zero were detected in populations; these results were consistent with self‐fertilization and clonal modes of reproduction for this pathogen. However, using Bayesian Markov chain Monte Carlo approach, principal component analysis and neighbour joining (NJ) algorithm, the Fujian P. sojae populations clustered into three distinct groups, one of which included most isolates of the northeast populations. What is more, significant estimates of pairwise fixation indices (FST) were detected between most populations, especially in different clusters. It is hypothesized that the cropping system used, the limited dispersal ability, and human‐mediated gene flow may account for the observed genetic structure of P. sojae populations in Fujian, China. In addition, a high virulence frequency of the pathogen on different cultivars carrying known major R genes for resistance, and a rapid increase in virulence frequency, indicated that these major R genes should not be used to manage seedling damping‐off and root rot diseases of soybean (Glycine max).

Reproduction and Pollination of the Endangered Dwarf Bear-PoppyArctomecon humilis(Papaveraceae) across a Quarter Century: Unraveling of a Pollination Web?

Arctomecon humilis, a rare gypsophile of the extreme northeastern Mojave Desert, is restricted to a few isolated populations in Washington County, Utah, USA. At several times in the past quarter century, we have studied the breeding system and reproductive success of this endangered species, recorded its pollinators, and tested the feasibility of human-assisted gene flow by performing reciprocal crosses between 2 isolated “populations” approximately 4 km apart. Arctomecon humilis possessed a mixed breeding system in the population studied (Beehive Dome in 1988); some plants exhibited self-compatibility but produced significantly fewer fruit/flowers and seeds/fruit for geitonogamous self-pollinations than for cross-pollinations. Few fruits and seeds were produced in the absence of pollinators. The results of cross-pollination treatments did not differ from unassisted open-pollinations (controls), suggesting that pollinators were not limiting reproductive success. Our more recent results (2012) suggest that some populations may be more at risk than others. Although all 7 populations surveyed produced ≥70% fruits/flower, they differed significantly in fruit set and in average seed number/fruit and seed weight. Possible reasons for these differences (i.e., inbreeding, genetic load, insufficient mating types, pollinator scarcity, etc.), are all potentially important for conservation management and should be investigated. Over the past 2 decades, the pollinator community appears to have changed dramatically from one composed of specialist and generalist bees to one where pollination is presently being accomplished by generalist foragers alone. The health of one of these generalists, the honey bee Apis mellifera, is a current global concern, and its future presence as a pollinator of A. humilis is unclear. Our reciprocal crosses between the White Dome and Webb Hill populations provide support for our proposal that human-mediated gene flow through interpopulation cross-pollinations be undertaken every 5 years to increase the genetic variability of populations. We make several other recommendations for research that would improve the ability of land managers to conserve this species.

Development and characterization of microsatellite markers in the coffee-family herb Ophiorrhiza japonica (Rubiaceae)

Ophiorrhiza japonica (Rubiaceae) in Taiwan shows altitudinal morphological differentiation, suggesting altitudinal genetic differentiation. However, global warming and/or road building are possibly causing human-mediated altitudinal gene flow and genetic disturbance. To investigate this possibility, we developed the first nuclear microsatellite markers for the genus. Using the low-cost compound microsatellite marker technique, 17 markers were developed and nine markers were polymorphic. The number of alleles per polymorphic locus ranged from 2 to 13. At population level, observed (Ho) and expected (He) heterozygosities ranged 0.070–0.831 and 0.068–0.812, respectively. The polymorphic information content ranged 0.066–0.787. No null allele, significant deviation from Hardy–Weinberg equilibrium, or significant linkage disequilibrium was observed. The 17 marker loci were successfully PCR-amplified in three congeneric species except for three cases. The developed microsatellite markers will be used to investigate genetic structure and gene flow among O. japonica populations at different altitudes.

Genetic diversity and differentiation in a wide ranging anadromous fish, American shad (Alosa sapidissima), is correlated with latitude

Studies that span entire species ranges can provide insight into the relative roles of historical contingency and contemporary factors that influence population structure and can reveal patterns of genetic variation that might otherwise go undetected. American shad is a wide ranging anadromous clupeid fish that exhibits variation in demographic histories and reproductive strategies (both semelparity and iteroparity) and provides a unique perspective on the evolutionary processes that govern the genetic architecture of anadromous fishes. Using 13 microsatellite loci, we examined the magnitude and spatial distribution of genetic variation among 33 populations across the species' range to (i) determine whether signals of historical demography persist among contemporary populations and (ii) assess the effect of different reproductive strategies on population structure. Patterns of genetic diversity and differentiation among populations varied widely and reflect the differential influences of historical demography, microevolutionary processes and anthropogenic factors across the species' range. Sequential reductions of diversity with latitude among formerly glaciated rivers are consistent with stepwise postglacial colonization and successive population founder events. Weak differentiation among U.S. iteroparous populations may be a consequence of human-mediated gene flow, while weak differentiation among semelparous populations probably reflects natural gene flow. Evidence for an effect of reproductive strategy on population structure suggests an important role for environmental variation and suggests that the factors that are responsible for shaping American shad life history patterns may also influence population genetic structure.

Extremely low genetic variability and highly structured local populations of Arabidopsis thaliana at higher latitudes

The genetic diversity and population structure of Arabidopsis thaliana populations from Norway were studied and compared to a worldwide sample of A. thaliana to investigate the demographic history and elucidate possible colonization routes of populations at the northernmost species limit. We genotyped 282 individuals from 31 local populations using 149 single nucleotide polymorphism markers. A high level of population subdivision (F(ST) = 0.85 ± 0.007) was found indicating that A. thaliana is highly structured at the regional level. Significant relationships between genetic and geographical distances were found, suggesting an isolation by distance mode of evolution. Genetic diversity was much lower, and the level of linkage disequilibrium was higher in populations from the north (65-68°N) compared to populations from the south (59-62°N); this is consistent with a northward expansion pattern. A neighbour-joining tree showed that populations from northern Norway form a separate cluster, while the remaining populations are distributed over a few minor clusters. Minimal gene flow seems to have occurred between populations in different regions, especially between the geographically distant northern and southern populations. Our data suggest that northern populations represent a homogenous group that may have been established from a few founders during northward expansions, while populations in the central part of Norway constitute an admixed group established by founders of different origins, most probably as a result of human-mediated gene flow. Moreover, Norwegian populations appeared to be homogenous and isolated compared to a worldwide sample of A. thaliana, but they are still grouped with Swedish populations, which may indicate common colonization histories.

Rapid parallel adaptive radiations from a single hybridogenic ancestral population

The Alpine lake whitefish (Coregonus lavaretus) species complex is a classic example of a recent radiation, associated with colonization of the Alpine lakes following the glacial retreat (less than 15 kyr BP). They have formed a unique array of endemic lake flocks, each with one to six described sympatric species differing in morphology, diet and reproductive ecology. Here, we present a genomic investigation of the relationships between and within the lake flocks. Comparing the signal between over 1000 AFLP loci and mitochondrial control region sequence data, we use phylogenetic tree-based and population genetic methods to reconstruct the phylogenetic history of the group and to delineate the principal centres of genetic diversity within the radiation. We find significant cytonuclear discordance showing that the genomically monophyletic Alpine whitefish clade arose from a hybrid swarm of at least two glacial refugial lineages. Within this radiation, we find seven extant genetic clusters centred on seven lake systems. Most interestingly, we find evidence of sympatric speciation within and parallel evolution of equivalent phenotypes among these lake systems. However, we also find the genetic signature of human-mediated gene flow and diversity loss within many lakes, highlighting the fragility of recent radiations.

Genetic diversity and population structure of the Chinese mitten crab Eriocheir sinensis in its native range

The Chinese mitten crab Eriocheir sinensis is an indigenous and economically important species in China, but can also be found as invasive species in Europe and America. Mitten crabs have been exploited extensively as a food resource since the 1990s. Despite its ecological and economic importance, the genetic structure of native mitten crab populations is not well understood. In this paper, we investigated the genetic structure of mitten crab populations in China by screening samples from ten locations covering six river systems at six microsatellite loci. Our results provide further evidence that mitten crabs from the River Nanliujiang in Southern China are a genetically differentiated population within the native range of Eriocheir, and should be recognized as a separate taxonomic unit. In contrast, extremely low levels of genetic differentiation and no significant geographic population structure were found among the samples located north of the River Nanliujiang. Based on the reproductive biology of mitten crabs and the geography of their habitat we argue that both natural and human-mediated gene flow are unlikely to fully account for the similar allele frequency distributions at microsatellite loci. Large population sizes of mitten crabs suggest instead that a virtual absence of genetic drift and significant homoplasy of microsatellite alleles have contributed to the observed pattern. Furthermore, a coalescent-based maximum likelihood method indicated a more than two-fold lower effective population size of the Southern population compared to the Northern Group and low but significant levels of gene flow between both areas.

Genetic diversity of Venturia inaequalis across Europe

The genetic diversity of eleven populations of Venturia inaequalis from five European countries was calculated based on the allele frequencies of 18 random amplified polymorphic DNA markers and the internal transcribed spacer region of the ribosomal DNA. Diversity within each population (HS) was high with values ranging from 0.26 to 0.33. Average differentiation among populations (GST) was 0.11 and populations were isolated by distance (r2=0.50, P<0.01). This indicates that extensive short-distance gene flow occurs in Europe and that dispersal over longer distances also appears to occur frequently enough to prevent differentiation due to genetic drift. We had expected more pronounced differentiation between populations north and south of the Alps, because V. inaequalis is primarily dispersed by rain splashing and wind distribution of leaf litter, and because the Alps might form a barrier to dispersal. However, our results indicate that human-mediated gene flow due to transport of spores or infected plant material has probably occurred.

Genetic structure in the perennial grasses Lolium perenne and Agrostis curtisii

Genetic variation was studied in unimproved grassland populations of two contrasting outbreeding perennial grass species. A total of 27 populations of Lolium perenne (perennial ryegrass) and 30 populations of Agrostis curtisii (bristle-leaved bent), sampled from seven and five regions spread across southern Britain, were assessed at three and four isozyme loci, respectively. The extent of genetic structure within and among populations was estimated using unbiased F-statistics. In A. curtisii, a nonagricultural species, populations from adjacent regions were found to be more genetically similar than those separated by greater distance. The reverse situation was observed within L. perenne, a species of major agricultural importance. It is suggested that the absence from L. perenne of the pattern of genetic variation found in A. curtisii is consistent with the occurrence of large-scale human-mediated gene flow via ‘improved’ ryegrass cultivars. If this is the case, then the disruption of natural patterns of genetic variation by the introduction of nonlocal genotypes may occur without apparent major ecological consequences.

The Virginia Partridge

Previous articleNext article FreeThe Virginia PartridgeAugustus FowlerAugustus Fowler Search for more articles by this author PDFPDF PLUS Add to favoritesDownload CitationTrack CitationsPermissionsReprints Share onFacebookTwitterLinkedInRedditEmail SectionsMoreDetailsFiguresReferencesCited by The American Naturalist Volume 3, Number 10Dec., 1869 Published for The American Society of Naturalists Article DOIhttps://doi.org/10.1086/270491 Views: 36Total views on this site Citations: 1Citations are reported from Crossref PDF download Crossref reports the following articles citing this article:Jeffrey G. Whitt, Jeff A. Johnson, Kelly S. Reyna Two centuries of human-mediated gene flow in northern bobwhites, Wildlife Society Bulletin 41, no.44 (Dec 2017): 639–648.https://doi.org/10.1002/wsb.829