Plant-associate interactions and diversification across trophic levels.

Plant patch structure and environmental context can influence the outcome of antagonistic and mutualistic plant-insect interactions, leading to spatially variable fitness effects for plants. We investigated the effects of herbivory and pollen limitation on plant reproductive performance in 28 patches of the self-compatible perennial herb Scrophularia nodosa and assessed how such effects varied with plant patch size, plant density and tree cover. Both antagonistic and mutualistic interactions had strong effects on plant reproductive performance. Leaf feeding from herbivores reduced both fruit production and seed germination, and leaf herbivory increased with plant patch size. Experimentally hand-pollinated flowers produced more seeds than open-pollinated flowers, and pollen limitation was more severe in patches with fewer plants. Our study on S. nodosa is one of few which documents that plant patch structure influences the outcome of both antagonistic and mutualistic plant-insect interactions. The results thus provide an example of how variation in plant patch structure and environmental factors can lead to spatially variable fitness effects from mutualistic and antagonistic interactions.

<p>Understanding the different types of genetic population structure that characterise marine species, and the processes driving such patterns, is crucial for establishing links between the ecology and evolution of a species. This knowledge is vital for management and conservation of marine species. Genetic approaches are a powerful tool for revealing ecologically relevant insights to marine population dynamics. Geographic patterns of genetic population structure are largely determined by the rate at which individuals are exchanged among populations (termed ‘population connectivity’), which in turn is influenced by conditions in the physical environment. The complexity of the New Zealand marine environment makes it difficult to predict how physical oceanographic and environmental processes will influence connectivity in coastal marine organisms and hence the type of genetic structure that will form. This complexity presents a challenge for management of marine resources but also makes the New Zealand region an interesting model system to investigate how and why population structure develops and evolves over time. Paphies subtriangulata (tuatua) and P. australis (pipi) are endemic bivalve ‘surf clams’ commonly found on New Zealand surf beaches and harbour/estuary environments, respectively. They form important recreational, customary and commercial fisheries, yet little is known about the stock structure of these species. This study aimed to use genetic techniques to determine population structure, levels of connectivity and ‘seascape’ genetic patterns in P. subtriangulata and P. australis, and to gain further knowledge of common population genetic processes operating in the New Zealand coastal marine environment. Eleven and 14 novel microsatellite markers were developed for P. subtriangulata and P. australis, respectively. Samples were collected from 10 locations for P. subtriangulata and 13 locations for P. australis (35-57 samples per location; total sample size of 517 for P. subtriangulata and 674 for P. australis). Geographic patterns of genetic variation were measured and rates of migration among locations were estimated on recent and historic time scales. Both species were characterised by genetic population structure that was consistent with their habitat. For P. subtriangulata, the Chatham Island population was strongly differentiated from the rest of the sampled locations. The majority of mainland locations were undifferentiated and estimated rates of migration among locations were high on both time scales investigated, although differentiation among some populations was observed. For P. australis, an overall isolation by distance (IBD) pattern was likely to be driven by distance between discrete estuary habitats. However, it was difficult to distinguish IBD from hierarchical structure as populations could be further subdivided into three significantly differentiated groups (Northern, South Eastern and South Western), providing evidence for barriers to dispersal. Further small scale patterns of genetic differentiation were observed in some locations, suggesting that complex current patterns and high self-recruitment drive small scale genetic population structure in both P. subtriangulata and P. australis. These patterns of genetic variation were used in seascape genetic analyses to test for associations with environmental variables, with the purpose of understanding the processes that might shape genetic population structure in these two species. Although genetic population structure varied between the two species, common physical and environmental variables (geographic distance, sea surface temperature, bed slope, tidal currents) are likely to be involved in the structuring of populations. Results suggest that local adaptation, in combination with restricted dispersal, could play a role in driving the small scale patterns of genetic differentiation seen among some localities. Overall, the outcomes of this research fill a gap in our knowledge about the rates and routes by which populations are connected and the environmental factors influencing such patterns in the New Zealand marine environment. Other studies have highlighted the importance of using multi-faceted approaches to understand complex processes operating in the marine environment. The present study is an important first step in this direction as these methods are yet to be widely applied to New Zealand marine species. Importantly, this study used a comparative approach, applying standardised methodology to compare genetic population structure and migration across species. Such an approach is necessary if we wish to build a robust understanding of the spatial and temporal complexities of population dynamics in the New Zealand coastal marine environment, and to develop effective management strategies for our unique marine species.</p>

<p>Understanding the different types of genetic population structure that characterise marine species, and the processes driving such patterns, is crucial for establishing links between the ecology and evolution of a species. This knowledge is vital for management and conservation of marine species. Genetic approaches are a powerful tool for revealing ecologically relevant insights to marine population dynamics. Geographic patterns of genetic population structure are largely determined by the rate at which individuals are exchanged among populations (termed ‘population connectivity’), which in turn is influenced by conditions in the physical environment. The complexity of the New Zealand marine environment makes it difficult to predict how physical oceanographic and environmental processes will influence connectivity in coastal marine organisms and hence the type of genetic structure that will form. This complexity presents a challenge for management of marine resources but also makes the New Zealand region an interesting model system to investigate how and why population structure develops and evolves over time. Paphies subtriangulata (tuatua) and P. australis (pipi) are endemic bivalve ‘surf clams’ commonly found on New Zealand surf beaches and harbour/estuary environments, respectively. They form important recreational, customary and commercial fisheries, yet little is known about the stock structure of these species. This study aimed to use genetic techniques to determine population structure, levels of connectivity and ‘seascape’ genetic patterns in P. subtriangulata and P. australis, and to gain further knowledge of common population genetic processes operating in the New Zealand coastal marine environment. Eleven and 14 novel microsatellite markers were developed for P. subtriangulata and P. australis, respectively. Samples were collected from 10 locations for P. subtriangulata and 13 locations for P. australis (35-57 samples per location; total sample size of 517 for P. subtriangulata and 674 for P. australis). Geographic patterns of genetic variation were measured and rates of migration among locations were estimated on recent and historic time scales. Both species were characterised by genetic population structure that was consistent with their habitat. For P. subtriangulata, the Chatham Island population was strongly differentiated from the rest of the sampled locations. The majority of mainland locations were undifferentiated and estimated rates of migration among locations were high on both time scales investigated, although differentiation among some populations was observed. For P. australis, an overall isolation by distance (IBD) pattern was likely to be driven by distance between discrete estuary habitats. However, it was difficult to distinguish IBD from hierarchical structure as populations could be further subdivided into three significantly differentiated groups (Northern, South Eastern and South Western), providing evidence for barriers to dispersal. Further small scale patterns of genetic differentiation were observed in some locations, suggesting that complex current patterns and high self-recruitment drive small scale genetic population structure in both P. subtriangulata and P. australis. These patterns of genetic variation were used in seascape genetic analyses to test for associations with environmental variables, with the purpose of understanding the processes that might shape genetic population structure in these two species. Although genetic population structure varied between the two species, common physical and environmental variables (geographic distance, sea surface temperature, bed slope, tidal currents) are likely to be involved in the structuring of populations. Results suggest that local adaptation, in combination with restricted dispersal, could play a role in driving the small scale patterns of genetic differentiation seen among some localities. Overall, the outcomes of this research fill a gap in our knowledge about the rates and routes by which populations are connected and the environmental factors influencing such patterns in the New Zealand marine environment. Other studies have highlighted the importance of using multi-faceted approaches to understand complex processes operating in the marine environment. The present study is an important first step in this direction as these methods are yet to be widely applied to New Zealand marine species. Importantly, this study used a comparative approach, applying standardised methodology to compare genetic population structure and migration across species. Such an approach is necessary if we wish to build a robust understanding of the spatial and temporal complexities of population dynamics in the New Zealand coastal marine environment, and to develop effective management strategies for our unique marine species.</p>

The genetic structure and diversity of plants may change significantly in an elevational gradient because different elevations regulate different ecological conditions. Several factors may influence genetic variation, such as mutations, selection, genetic drift, and gene flow. The aim of the present study was to evaluate the genetic structure and diversity of populations of Tibouchina pulchra Cogn. (Melastomataceae) trees in two extremes of an elevational gradient experiencing different environmental conditions. Nine polymorphic microsatellite loci were used to measure the genetic diversity of 14 adult populations, whose structure was evaluated using frequentist and Bayesian analyses. We also carried out progeny structure and paternity analyses comparing the number of fathers of each progeny and the probability of the progeny genotypes to be the result of selfing in order to evaluate the possible current processes leading to such genetic structure. Genetic structure analyses indicated the existence of genetic differentiation between populations in adults and progenies, but with a contact interface between them. The population from the higher region showed smaller genetic diversity when compared to the population at the lower region. However, the pollen variability delivered to the stigmas at the higher region was not different from that of the lower region. These results may be explained by the dynamics of gene flow mediated by pollen, especially by the different amounts of pollination events in each region, as well as local adaptation, distribution, and reproduction characteristics of T. pulchra.

Proportioning Whole-Genome Single-Nucleotide–Polymorphism Diversity for the Identification of Geographic Population Structure and Genetic Ancestry

Wild sorghums are extremely diverse phenotypically, genetically and geographically. However, there is an apparent lack of knowledge on the genetic structure and diversity of wild sorghum populations within and between various eco-geographical regions. This is a major obstacle to both their effective conservation and potential use in breeding programs. The objective of this study was to assess the genetic diversity and structure of wild sorghum populations across a range of eco-geographical conditions in Kenya. Sixty-two wild sorghum populations collected from the 4 main sorghum growing regions in Kenya were genotyped using 18 simple sequence repeat markers. The study showed that wild sorghum is highly variable with the Coast region displaying the highest diversity. Analysis of molecular variance showed a significant variance component within and among wild sorghum populations within regions. The genetic structure of wild sorghum populations indicated that gene flow is not restricted to populations within the same geographic region. A weak regional differentiation was found among populations, reflecting human intervention in shaping wild sorghum genetic structure through seed-mediated gene flow. The sympatric occurrence of wild and cultivated sorghums coupled with extensive seed-mediated gene flow, suggests a potential crop-to-wild gene flow and vice versa across the regions. Wild sorghum displayed a mixed mating system. The wide range of estimated outcrossing rates indicate that some environmental conditions may exist where self-fertilisation is favoured while others cross-pollination is more advantageous.

Population genetic diversity and structure of the pecan scab pathogen, <i>Venturia effusa</i>, on cv. Desirable and native seedlings, and the impact of marker number

Understanding population genetic structure and its possible causal factors is critical for utilizing genetic resources and genetic breeding of economically important plants. Although Torreya grandis is an important conifer producing nuts in China, little is known about its population structure, let alone the causal factors that shaped its genetic variation pattern and population structure. In this work, we intended to characterize the genetic variation pattern and population structure of the nut-yielding conifer T. grandis throughout its whole geographical distribution and further explore the potentially causal factors for the population structure using multiple approaches. A moderate level of genetic diversity and a novel population structure were revealed in T. grandis based on eleven robust EST-SSR loci and three chloroplast fragments. Alien genetic composition derived from the closely related species T. nucifera endemic to Japan was detected in the Kuaiji Mountain area, where the seed quality of T. grandis is considered the best in China. Demography history and niche modeling were inferred and performed, and the contribution of geographic isolation to its population structure was compared with that of environmental isolation. Significant demographic changes occurred, including a dramatic population contraction during the Quaternary, and population divergence was significantly correlated with geographic distance. These results suggested that early breeding activities and demographic changes significantly contributed to the population structure of T. grandis. In turn, the population structure was potentially associated with the excellent variants and adaptation of cultivars of T. grandis. The findings provide important information for utilizing genetic resources and genetic breeding of T. grandis in the future.

Advances in molecular techniques have enabled the study of genetic diversity and population structure in many different contexts. Studies that assess the genetic structure of cetacean populations often use biopsy samples from free-ranging individuals and tissue samples from stranded animals or individuals that became entangled in fishery or aquaculture equipment. This leads to the question of how representative the location of a stranded or entangled animal is with respect to its natural range, and whether similar results would be obtained when comparing carcass samples with samples from free-ranging individuals in studies of population structure. Here we use tissue samples from carcasses of dolphins that stranded or died as a result of bycatch in South Australia to investigate spatial population structure in two species: coastal bottlenose (Tursiops sp.) and short-beaked common dolphins (Delphinus delphis). We compare these results with those previously obtained from biopsy sampled free-ranging dolphins in the same area to test whether carcass samples yield similar patterns of genetic variability and population structure. Data from dolphin carcasses were gathered using seven microsatellite markers and a fragment of the mitochondrial DNA control region. Analyses based on carcass samples alone failed to detect genetic structure in Tursiops sp., a species previously shown to exhibit restricted dispersal and moderate genetic differentiation across a small spatial scale in this region. However, genetic structure was correctly inferred in D. delphis, a species previously shown to have reduced genetic structure over a similar geographic area. We propose that in the absence of corroborating data, and when population structure is assessed over relatively small spatial scales, the sole use of carcasses may lead to an underestimate of genetic differentiation. This can lead to a failure in identifying management units for conservation. Therefore, this risk should be carefully assessed when planning population genetic studies of cetaceans.

BackgroundEthiopian sheep living in different climatic zones and having contrasting morphologies are a most promising subject of molecular-genetic research. Elucidating their genetic diversity and genetic structure is critical for designing appropriate breeding and conservation strategies.ObjectiveThe study was aimed to investigate genome-wide genetic diversity and population structure of eight Ethiopian sheep populations.MethodsA total of 115 blood samples were collected from four Ethiopian sheep populations that include Washera, Farta and Wollo (short fat-tailed) and Horro (long fat-tailed). DNA was extracted using Quick-DNA™ Miniprep plus kit. All DNA samples were genotyped using Ovine 50 K SNP BeadChip. To infer genetic relationships of Ethiopian sheep at national, continental and global levels, genotype data on four Ethiopian sheep (Adilo, Arsi-Bale, Menz and Black Head Somali) and sheep from east, north, and south Africa, Middle East and Asia were included in the study as reference.ResultsMean genetic diversity of Ethiopian sheep populations ranged from 0.352 ± 0.14 for Horro to 0.379 ± 0.14 for Arsi-Bale sheep. Population structure and principal component analyses of the eight Ethiopian indigenous sheep revealed four distinct genetic cluster groups according to their tail phenotype and geographical distribution. The short fat-tailed sheep did not represent one genetic cluster group. Ethiopian fat-rump sheep share a common genetic background with the Kenyan fat-tailed sheep.ConclusionThe results of the present study revealed the principal component and population structure follows a clear pattern of tail morphology and phylogeography. There is clear signature of admixture among the study Ethiopian sheep populations

Genetic diversity and population structure of 88 Chinese Lentinula edodes strains belonging to four geographic populations were inferred from 68 Insertion-Deletion (InDel) and two simple sequence repeat (SSR) markers. The overall values of Shannon’s information index and gene diversity were 0.836 and 0.435, respectively, demonstrating a high genetic diversity in Chinese L. edodes strains. Among the four geographic populations, the Central China population displayed a lower genetic diversity. Multiple analyses resolved two unambiguous genetic groups that corresponded to two regions from which the samples were collected—one was a high-altitude region (region 1) and the other was a low-altitude region (region 2). Results from analysis of molecular variance suggested that the majority of genetic variation was contained within populations (74.8 %). Although there was a strong genetic differentiation between populations (F ST = 0.252), the variability of ITS sequences from representative strains of the two regions (<3 %) could not support the existence of cryptic species. Pairwise F ST values and Nei’s genetic distances showed that there were relatively lower genetic differentiations and genetic distances between populations from the same region. Geographic distribution could play a vital role in the formation of the observed population structure. Mycelium growth rate and precocity of L. edodes strains displayed significant differences between the two regions. Strains from region 2 grew faster and fructified earlier, which could be a result of adaptation to local environmental factors. To the best of our knowledge, this was the first study on the genetic structure and differentiation between populations, as well as the relationship between genetic structure and phenotypic traits in L. edodes.

BackgroundRivers and streams facilitate movement of individuals and their genes across the landscape and are generally recognized as dispersal corridors for riparian plants. Nevertheless, some authors have reported directly contrasting results, which may be attributed to a complex mixture of factors, such as the mating system and dispersal mechanisms of propagules (seed and pollen), that make it difficult to predict the genetic diversity and population structure of riparian species. Here, we investigated a riparian self-fertilizing herb Caulokaempferia coenobialis, which does not use anemochory or zoochory for seed dispersal; such studies could contribute to an improved understanding of the effect of rivers or streams on population genetic diversity and structure in riparian plants. Using polymorphic ISSR and cpDNA loci, we studied the effect at a microgeographic scale of different stream systems (a linear stream, a dendritic stream, and complex transverse hydrological system) in subtropical monsoon forest on the genetic structure and connectivity of C. coenobialis populations across Dinghu Mountain (DH) and Nankun Mountain (NK).ResultsThe results indicate that the most recent haplotypes (DH: H7, H8; NK: h6, h7, h11, h12) are not shared among local populations of C. coenobialis within each stream system. Furthermore, downstream local populations do not accumulate genetic diversity, whether in the linear streamside local populations across DH (H: 0.091 vs 0.136) or the dendritic streamside local populations across NK (H: 0.079 vs 0.112, 0.110). Our results show that the connectivity of local C. coenobialis populations across DH and NK can be attributed to historical gene flows, resulting in a lack of spatial genetic structure, despite self-fertilization. Selfing C. coenobialis can maintain high genetic diversity (H = 0.251; I = 0.382) through genetic differentiation (GST = 0.5915; FST = 0.663), which is intensified by local adaptation and neutral mutation and/or genetic drift in local populations at a microgeographic scale.ConclusionWe suggest that streams are not acting as corridors for dispersal of C. coenobialis, and conservation strategies for maintaining genetic diversity of selfing species should be focused on the protection of all habitat types, especially isolated fragments in ecosystem processes.

We tested the hypothesis that dispersal is sex biased in an unexploited population of brook trout, Salvelinus fontinalis, on Cape Race, Newfoundland, Canada. Based on the assumptions that trout are promiscuous and that reproductive success is limited primarily by either number of mates (males) or fecundity (females), we predicted that males would disperse greater distances than females. We also tested the hypothesis that trout populations comprise stationary and mobile individuals, predicting that males have greater mobility than females. Based on a mark-recapture study of 943 individually tagged fishes, 191 of which were recaptured over 5 years, we find strong support for our hypothesis of male-biased dispersal in brook trout. Averaged among all 11 resampling periods, males dispersed 2.5 times as far as females; during the spawning period only, male dispersal exceeded that by females almost fourfold. Both sexes were heterogeneous with respect to movement, with a lower incidence of mobility among females (29.6%) than males (41.1%); mobile males dispersed six times further than mobile females. We conclude that this sex bias reduces mate competition among male kin and decreases the probability that males will reproduce with related females.

BackgroundUnderstanding the genetic structure and local adaptive evolutionary mechanisms of marine organisms is crucial for the management of biological resources. As the ecologically and commercially important small-sized shallow-sea fish, Collichthys lucidus plays a vital role in the structure and functioning of marine ecosystem processes. C. lucidus has been shown to have an obvious population structure. Therefore, it is an ideal candidate for investigating population differentiation and local adaptation under heterogeneous environmental pressure.ResultsA total of 184,708 high-quality single nucleotide polymorphisms (SNPs) were identified and applied to elucidate the fine-scale genetic structure and local thermal adaptation of 8 C. lucidus populations. Population structure analysis based on all SNPs indicated that the northern group and southern group of C. lucidus have a strong differentiation. Moreover, 314 SNPs were found to be significantly associated with temperature variation, and annotations of genes containing temperature-related SNPs suggested that genes were involved in material (protein, lipid, and carbohydrate) metabolism and immune responses.ConclusionThe high genetic differentiation of 8 C. lucidus populations may have been caused by long-term geographic isolation during the glacial period. Moreover, we suspected that variation in these genes associated with material (protein, lipid, and carbohydrate) metabolism and immune responses was critical for adaptation to spatially heterogeneous temperatures in natural C. lucidus populations. In conclusion, this study could help us determine how C. lucidus populations will respond to future ocean temperature rising.

Knowledge about genetic diversity and population structure among goat populations is essential for understanding environmental adaptation and fostering efficient utilization, development, and conservation of goat breeds. Uganda's indigenous goats exist in three phenotypic groups: Mubende, Kigezi, and Small East African. However, a limited understanding of their genetic attributes and population structure hinders the development and sustainable utilization of the goats. Using the Goat Illumina 60k chip International Goat Genome Consortium V2, the whole-genome data for 1,021 indigenous goats sourced from 10 agroecological zones in Uganda were analyzed for genetic diversity and population structure. A total of 49,337 (82.6%) single-nucleotide polymorphism markers were aligned to the ARS-1 goat genome and used to assess the genetic diversity, population structure, and kinship relationships of Uganda's indigenous goats. Moderate genetic diversity was observed. The observed and expected heterozygosities were 0.378 and 0.383, the average genetic distance was 0.390, and the average minor allele frequency was 0.30. The average inbreeding coefficient (Fis) was 0.014, and the average fixation index (Fst) was 0.016. Principal component analysis, admixture analysis, and discriminant analysis of principal components grouped the 1,021 goat genotypes into three genetically distinct populations that did not conform to the known phenotypic populations but varied across environmental conditions. Population 1, comprising Mubende (90%) and Kigezi (8.1%) goats, is located in southwest and central Uganda, a warm and humid environment. Population 2, which is 59% Mubende and 49% Small East African goats, is located along the Nile Delta in northwestern Uganda and around the Albertine region, a hot and humid savannah grassland. Population 3, comprising 78.4% Small East African and 21.1% Mubende goats, is found in northeastern to eastern Uganda, a hot and dry Commiphora woodlands. Genetic diversity and population structure information from this study will be a basis for future development, conservation, and sustainable utilization of Uganda's goat genetic resources.