Evidence Of Genetic Differentiation Research Articles

Intraspecific divergence in a coastal plant, Euphorbia jolkinii, at a major biogeographic boundary in East Asia.

Quaternary climatic fluctuations and long-distance seed dispersal across the sea are critical factors affecting the distribution of coastal plants, but the spatiotemporal nature of population expansion and distribution change of East Asian coastal plants during this period are rarely examined. To explore this process, we investigated the genome-wide phylogenetic patterns of Euphorbia jolkinii Boiss. (Euphorbiaceae), which grows widely on littoral areas of Japan, Korea, and Taiwan. We used plastome sequences and genome-wide single nucleotide polymorphisms in samples across the species range to reveal phylogeographic patterns and spatiotemporal distributional changes. We conducted ecological niche modeling for the present and the last glacial maximum (LGM). Genetic differentiation was observed between the northern and southern populations of E. jolkinii, separated by the major biogeographic boundary, the Tokara Gap. These two groups of populations differentiated during the glacial period and subsequently intermingled in the intermorainic areas of the central Ryukyu Islands after the LGM. Ecological niche models suggested that the potential range of E. jolkinii was restricted to southern Kyushu; however, it was widespread in the southern Ryukyu Islands and Taiwan during the LGM. This study provides evidence of genetic differentiation among coastal plant populations separated by the prominent biogeographical boundary. Although coastal plants are typically expected to maintain population connectivity through sea-drifted seed dispersal, our findings suggest that genetic differences may arise because of a combination of limited gene flow and changes in climate during the glacial period.

Occurrence of giant migratory locust Locusta migratoria (Acrididae) on Tsushima Island, Japan

This study focused on the populations of Locusta migratoria (Linnaeus, 1758) on Tsushima Island, Japan, which exhibited the largest mean adult body size when compared to other populations from various climatic regions. Certain individuals, designated as “giant locusts,” displayed exceptionally large sizes, with females and males identified when with head widths surpassing 10.5 mm and 8.0 mm, respectively. The maximum weight recorded for a giant locust was 8.9 g, in contrast to other examined females with the maximum weight ranging from 3.1 to 5.5 g. Notably, giant females exhibited the ability to yield larger egg pods and progeny compared to their counterparts. A positive correlation emerged between body size of adult females and the number of ovarioles. To explore the potential heritability of body size, selection experiments were conducted across two generations. A significant impact of selection on adult body size was apparent at LD 12:12h, whereas this effect was not evident at LD 16:8h. Furthermore, crossing experiments showed that body size at hatching closely resembled that of the female parent or demonstrated dimensions intermediary between the two parents, suggesting a complex genetic basis for the observed body size variations. This study provides no evidence of genetic differentiation between the giant locusts and the other locusts on this island.

Lack of genetic structure in euryhaline Chelon labrosus from the estuaries under anthropic pressure in the Southern Bay of Biscay to the coastal waters of the Mediterranean Sea

Over the last decade, xenoestrogenic effects have been reported in populations of thicklip grey mullet Chelon labrosus from contaminated estuaries in the Bay of Biscay, resulting in intersex condition. To understand the level of gene flow in individuals of different Basque estuaries microsatellite markers were used to evaluate the population structure and connectivity of C. labrosus from estuaries of the Basque coast. 46 microsatellites were tested and 10 validated for the analysis of 204 individuals collected from 5 selected Basque estuaries and 2 outgroups in the Bay of Cadiz and Thermaic Gulf. The polymorphic microsatellites revealed 74 total alleles, 2–19 alleles per locus. The mean observed heterozygosity (0.49 ± 0.02) was lower than the expected one (0.53 ± 0.01). There was no evidence of genetic differentiation (FST = 0.0098, P = 0.0000) among individuals or sites. Bayesian clustering analysis revealed a single population in all sampled locations. The results of this study indicate widespread genetic homogeneity and panmixia of C. labrosus across the current sampling areas spanning the Atlantic and Mediterranean basins. The hypothesis of panmixia could therefore be well supported so individuals inhabiting estuaries with high prevalence of intersex condition should be considered as members of the same single genetic group as those inhabiting adjacent estuaries without incidence of xenoestrogenicity.

Anthropogenic influences on genetic diversity and differentiation of the clearhead icefish (Protosalanx hyalocranius), as revealed by mitochondrial and microsatellite DNA markers

The clearhead icefish, Protosalanx hyalocranius, is an economically important fishery species in China. For the past few decades, the wild resources of P. hyalocranius have markedly decreased due to human activities such as overfishing, hydro-projects and water pollution. Meanwhile, P. hyalocranius has been widely introduced into lakes and reservoirs of northern China and some have become established, invasive populations, leading to detrimental effects on ecosystems. Using mitochondrial control region sequences and nine microsatellite DNA markers, the aim of this study was to assess to what extent human activities could impact the genetic diversity and population structure of P. hyalocranius, and explore the sources of the invasive Heilong River population based on genetic characterization. Based on mitochondrial DNA, the average haplotype diversity and nucleotide diversity among six populations were 0.737 and 0.0029 respectively. Based on microsatellite markers, the observed (HO) and expected (HE) heterozygosities in each population ranged from 0.481 to 0.565 and 0.478 to 0.565, respectively. Both mitochondrial and microsatellite markers indicated the genetic diversity in Chaohu Lake was the lowest. HO and HE of the two anadromous populations (Liao River Estuary and Yalu River Estuary) were close to Chaohu Lake and relatively low among all populations. The pairwise Dest values showed high and significant genetic differentiation between Taihu Lake and other populations. There was no evidence of genetic differentiation between Chaohu Lake and the two anadromous populations. No significant reduction of genetic diversity was observed in the Heilong River population. Bottleneck analysis showed that the two anadromous populations may have experienced a recent genetic bottleneck. DIYABC analysis suggested that the sources of the invasive Heilong River population were Taihu and Hongze lakes, with a greater genetic contribution from Hongze Lake. Therefore, the anadromous populations of P. hyalocranius may have suffered more impacts from human activities than the strictly freshwater populations. Among freshwater populations, Chaohu Lake should also be paid more attention in fisheries management. In addition, our study demonstrated that multiple introductions can give rise to high genetic diversity in an invasive population.

Subspecies differentiation and range-wide genetic structure are driven by climate in the California gnatcatcher, a flagship species for coastal sage scrub conservation.

Understanding genetic structure and diversity within species can uncover associations with environmental and geographic attributes that highlight adaptive potential and inform conservation and management. The California gnatcatcher, Polioptila californica, is a small songbird found in desert and coastal scrub habitats from the southern end of Baja California Sur to Ventura County, California. Lack of congruence among morphological subspecies hypotheses and lack of measurable genetic structure found in a few genetic markers led to questions about the validity of subspecies within P. californica and the listing status of the coastal California gnatcatcher, P. c. californica. As a U.S. federally threatened subspecies, P. c. californica is recognized as a flagship for coastal sage scrub conservation throughout southern California. We used restriction site‐associated DNA sequencing to develop a genomic dataset for the California gnatcatcher. We sampled throughout the species' range, examined genetic structure, gene–environment associations, and demographic history, and tested for concordance between genetic structure and morphological subspecies groups. Our data support two distinct genetic groups with evidence of restricted movement and gene flow near the U.S.‐ Mexico international border. We found that climate‐associated outlier loci were more strongly differentiated than climate neutral loci, suggesting that local climate adaptation may have helped to drive differentiation after Holocene range expansions. Patterns of habitat loss and fragmentation are also concordant with genetic substructure throughout the southern California portion of the range. Finally, our genetic data supported the morphologically defined P. c. californica as a distinct group, but there was little evidence of genetic differentiation among other previously hypothesized subspecies in Baja California. Our data suggest that retaining and restoring connectivity, and protecting populations, particularly at the northern range edge, could help preserve existing adaptive potential to allow for future range expansion and long‐term persistence of the California gnatcatcher.

The first evidence for genetic differentiation of a non-native false mussel Mytilopsis sallei (Récluz, 1849) in southern Thailand.

ABSTRACT The false mussel Mytilopsis sallei (Récluz, 1849) is a bivalve indigenous to the tropical western Atlantic that has become invasive in Southeast-Asia. Establishment of M. sallei populations in Thailand was reported in 2008 and it has spread to several locations along both the Gulf of Thailand and Andaman Sea coasts. The survival of planktonic larvae of M. sallei in oceanic salinity is known to be poor so these populations may be a result of multiple introductions, and propagule exchanges between populations may be limited. To test this, we investigated the variability of cytochrome oxidase subunit I in M. sallei within and between spatially isolated locations, as well as between the Gulf of Thailand and Andaman Sea coasts. In total, 407 base pairs from 60 individuals across five locations were analysed. Differences in the genetic structure of M. sallei among the five populations from southern Thailand suggest that there is no connectivity between the Gulf of Thailand and Andaman Sea populations. The results revealed the presence of six of the 15 haplotypes known among Southeast-Asian populations of M. sallei. This study contributes to the understanding of population genetic structure of the non-native false mussel, M. sallei, in Southeast-Asia.

Multispecies colour polymorphisms associated with contrasting microhabitats in two Mediterranean wrasse radiations.

Intraspecific colour polymorphisms (CPs) present unique opportunities to study fundamental evolutionary questions, such as the link between ecology and phenotype, mechanisms maintaining genetic diversity and their putative role in speciation. Wrasses are highly diverse in ecology and morphology and harbour a variety of colour‐polymorphic species. In the Mediterranean Sea, wrasses of the tribe Labrini evolved two species radiations each harbouring several species with a brown and a green morph. The colour morphs occur in complete sympatry in mosaic habitats with rocky outcrops and Neptune grass patches. Morph‐specific differences had not been characterized yet and the evolutionary forces maintaining them remained unknown. With genome‐wide data for almost all Labrini species, we show that species with CPs are distributed across the phylogeny, but show evidence of hybridization. This suggests that the colour morphs are either ancient and have been lost repeatedly, that they have evolved repeatedly or have been shared via hybridization. Focusing on two polymorphic species, we find that each colour morph is more common in the microhabitat providing the best colour match and that the morphs exhibit additional behavioural and morphological differences further improving crypsis in their respective microhabitats. We find little evidence for genetic differentiation between the morphs in either species. Therefore, we propose that these colour morphs represent a multi‐niche polymorphism as an adaptation to the highly heterogeneous habitat. Our study highlights how colour polymorphism (CP) can be advantageous in mosaic habitats and that Mediterranean wrasses are an ideal system to study trans‐species polymorphisms, i.e. polymorphisms maintained across several species, in adaptive radiations.

Genetic population structure of summer flounder Paralichthys dentatus using microsatellite DNA analysis

Summer flounder Paralichthys dentatus supports one of the most valuable commercial and recreational fisheries along the Atlantic Coast of the U.S. However, in recent decades the management of this species has proven to be one of the most contentious for any exploited marine resource in the region. A coastwide catch quota is imposed annually for summer flounder of which 60% is allocated to the commercial fishery and 40% to the recreational fishery. The allocation is further divided among the individual coastal states from North Carolina to Massachusetts based on their landings in the 1980s. This process, based on political jurisdictions, does not consider the species’ biological stock structure. Previous genetic studies (allozyme, mtDNA, and SNPs) provided contradictory results regarding the possible population structure of summer. To address this issue, we used DNA microsatellite analysis at 9 loci to define the coastwide population structure of summer flounder. In total, 1182 specimens were analyzed from 18 collection sites. Most collections were from the Continental Shelf during the fall-winter spawning season. These were supplemented with additional samples from inshore waters from North Carolina to Florida, and inshore sites which support significant recreational fisheries at Nantucket Shoals, Massachusetts and Fire Island, New York. The overall level of genetic differentiation in pairwise comparisons between collections was very low, mean FST= 0.001. There was no evidence of genetic differentiation between collections from north and south of Cape Hatteras. Our microsatellite results are consistent with an earlier SNP study which failed to find significant allelic heterogeneity among coastwide collections of summer flounder. However, a subset of pairwise FST comparisons between some collections proved statistically significant. Furthermore, in STRUCTURE analysis we found evidence of two genetic clusters within the species’ northern landings area, however, this finding was not supported by DPAC analysis. We conclude that summer flounder most likely constitute a single population along their entire Atlantic Coast distribution.

Genetic Diversity and Population Structure of the Asian Tiger Mosquito (Aedes albopictus) in Vietnam: Evidence for Genetic Differentiation by Climate Region.

Aedes albopictus is a native mosquito to Southeast Asia with a high potential for disease transmission. Understanding how Ae. albopictus populations that develop in the species’ native range is useful for planning future control strategies and for identifying the sources of invasive ranges. The present study aims to investigate the genetic diversity and population structure of Ae. albopictus across various climatic regions of Vietnam. We analyzed mitochondrial cytochrome oxidase I (COI) gene sequences from specimens collected from 16 localities, and we used distance-based redundancy analysis to evaluate the amount of variation in the genetic distance that could be explained by both geographic distance and climatic factors. High levels of genetic polymorphism were detected, and the haplotypes were similar to those sequences from both temperate and tropical regions worldwide. Of note, these haplotype groups were geographically distributed, resulting in a distinct population structure in which northeastern populations and the remaining populations were genetically differentiated. Notably, genetic variation among the Ae. albopictus populations was driven primarily by climatic factors (64.55%) and to a lesser extent was also influenced by geographic distance (33.73%). These findings fill important gaps in the current understanding of the population genetics of Ae. albopictus in Vietnam, especially with respect to providing data to track the origin of the invaded regions worldwide.

Population genetics of Bull Trout (Salvelinus confluentus) in the upper Athabasca River basin.

Freshwater ecosystems are negatively impacted by a variety of anthropogenic stressors, with concomitant elevated rates of population decline for freshwater aquatic vertebrates. Because reductions in population size and extent can negatively impact genetic diversity and gene flow, which are vital for sustained local adaptation, it is important to measure these characteristics in threatened species that may yet be rescued from extinction. Across its native range, Bull Trout (Salvelinus confluentus) extent and abundance are in decline due to historic overharvest, invasive non‐native species, and habitat loss. In Alberta's Eastern Slope region, populations at the range margin have progressively been lost, motivating us to better understand the amount and distribution of genetic variation in headwater habitats and some downstream sites where they continue to persist. Across this region, we sampled 431 Bull Trout from 20 sites in the Athabasca and Saskatchewan River basins and assayed 10 microsatellite loci to characterize within‐ and among‐population genetic variation. The Saskatchewan and Athabasca River basins contained similar levels of heterozygosity but were differentiated from one another. Within the Athabasca River basin, five genetically differentiated clusters were found. Despite the evidence for genetic differentiation, we did not observe significant isolation‐by‐distance patterns among these sites. Our findings of ample genetic diversity and no evidence for hybridization with non‐native Brook Trout in headwater habitats provide motivation to ameliorate downstream habitats and remove anthropogenic barriers to connectivity towards the goal of long‐term persistence of this species.

Isoëtes sabatina (Isoëtaceae, Lycopodiopsida): Taxonomic distinctness and preliminary ecological insights

Abstract Isoëtes sabatina is the rarest aquatic quillwort in Europe. Although recently found (2013) in Lake Bracciano (central Italy), the species is just one step away from extinction with an estimated population not exceeding 400 individuals and a spatial range of a few hundred square metres. Lake Bracciano is a deep, oligo‐mesotrophic Mediterranean volcanic lake that has been subjected to human activities. From January to October 2017, the lake experienced a dramatic water level decrease (up to −1.50 m), which significantly affected the littoral zone and the habitat of I. sabatina. To improve the chances of survival of I. sabatina, the first eco‐taxonomic investigation on this species was carried out to describe its genetic distinctness, physical and chemical requirements and companion species. The phylogenetic position of I. sabatina was investigated by applying standard DNA barcoding methods. Simultaneously, during summer 2019, the physical and chemical features of water and sediments of the I. sabatina population and five small Alpine lakes colonized by Isoëtes echinospora – a supposed close relative – were characterized. These data were then compared with the available data on the trophic requirements of the target obligate aquatic Isoëtes, together with Isoëtes lacustris and Isoëtes malinverniana. The present survey confirmed the taxonomic and ecological distinctness of I. sabatina – providing the first evidence of genetic differentiation from I. echinospora. Isoëtes sabatina grows in waters with temperature, conductivity and total alkalinity up to 30°C, 561 μS cm−1 and 3.45 meq L−1, respectively. The edaphic requirements of I. sabatina confirm its outstanding conservation value, and this study offers a basic understanding of how to prevent its extinction. Now, all possible actions must be taken immediately to save this species.

Genetic structure of urban and non-urban populations differs between two common parid species

Landscape conversions induced by human activities can affect dispersal patterns of various bird species and, as a result, affect genetic structure of their populations. Genetic differentiation of bird populations may be enhanced by habitat variation, especially in urban-non-urban systems. The majority of population genetic studies focus on single species, which inflicts limitations for direct comparisons of genetic responses of avian populations to urbanization. Here, we used a set of microsatellite markers to examine genetic diversity, gene flow and population structure in two common parid species, great tits Parus major and blue tits Cyanistes caeruleus occupying three sites in habitats with contrasting urbanization level in central Poland. We found low but significant divergence of urban park population with both suburban and non-urban forest great tit populations, while no differentiation was found between suburban forest and non-urban forest populations. In contrast, no evidence for genetic differentiation was found between blue tit populations from the urban park, suburban forest and non-urban forest sites. We conclude that great tits and blue tits respond to urbanization-related changes in a different way, which may be a result of different rates of migration and/or dispersal, likely higher in blue tits. Some impact may be also induced by interspecific competition. We suggest that changing the focus of urban genetic research from single to multiple species may provide novel insights into how natural populations respond to the processes of urbanization.

Conservation concerns associated with low genetic diversity for K\u2019gari\u2013Fraser Island dingoes

The dingo population on world heritage-listed K’gari-Fraser Island (K’gari) is amongst the most well-known in Australia. However, an absence of population genetic data limits capacity for informed conservation management. We used 9 microsatellite loci to compare the levels of genetic diversity and genetic structure of 175 K’gari dingo tissue samples with 264 samples from adjacent mainland regions. Our results demonstrated that the K'gari population has significantly lower genetic diversity than mainland dingoes (AR, HE, PAR; p < 0.05) with a fourfold reduction in effective population size (Ne = 25.7 vs 103.8). There is also strong evidence of genetic differentiation between the island and mainland populations. These results are in accordance with genetic theory for small, isolated, island populations, and most likely the result of low initial diversity and founder effects such as bottlenecks leading to decreased diversity and drift. As the first study to incorporate a large sample set of K’gari dingoes, this provides invaluable baseline data for future research, which should incorporate genetic and demographic monitoring to ensure long-term persistence. Given that human-associated activities will continue to result in dingo mortality, it is critical that genetic factors are considered in conservation management decisions to avoid deleterious consequences for this iconic dingo population.

Systematics of Hyperolius mitchelli Loveridge, 1953 and Hyperolius rubrovermiculatus Schiøtz, 1975 (Anura: Hyperoliidae) and assignment of populations from northern Tanzania

ABSTRACT The taxonomic validity of the East African reed frogs Hyperolius mitchelli Loveridge, 1953 and Hyperolius rubrovermiculatus Schiøtz, 1975 has been questioned in the literature, with the latter having been recognised as a distinct lineage, but also synonymised as a colour variant of H. mitchelli. The recent description of a new closely related congener from Mozambique, Hyperolius stictus (Conradie et al., 2018), along with evidence of genetic differentiation within H. mitchelli has suggested that this widely distributed species might be a species complex. In this study, we reassess the relationships of these closely related species with new field sampling, molecular, morphological and bioacoustics analyses with the aim to assign the correct taxonomic identity to H. cf. mitchelli from northern Tanzania. Our results demonstrate that there are four distinct lineages within this group: H. stictus from Mozambique; H. rubrovermiculatus from southern Kenya; H. mitchelli sensu stricto from central and southern Tanzania and Malawi and H. cf. mitchelli from north-eastern Tanzania. Based on our combined analyses we assign H. cf. mitchelli as a new population of H. rubrovermiculatus with distinct colouration, extending the range of this species from Kenya into northern Tanzania. We also clarify the genetic, morphological and acoustic variation within and between all lineages to further knowledge of this group and provide direction for future study into this fragmented and variable lineage.

Development of microsatellite markers and genetic diversity in wild and cultured populations of black carp (Mylopharyngodon piceus) along the Yangtze River

Black carp (Mylopharyngodon piceus) is one of traditionally important aquaculture fishes in China; however, population genetic studies are relatively rare for this species. In the present study, we developed a set of microsatellite markers by FIASCO method and used ten of these polymorphic markers to evaluate genetic diversity of black carp (three wild populations and six cultured populations including larvae from fish seed farms and adults from fish markets, n = 269) along the Yangtze River basin. Among these samples, mean number of alleles (Na) and effective number of alleles (Ne) were 14 and 6, respectively. Genetic diversities of wild populations were higher than that of cultured populations, represented by Ho of 0.767 vs 0.730, He of 0.806 vs 0.722, and polymorphism information content of 0.767 vs 0.6731, respectively, although a few cultured populations were exceptional. Fst from 0.010 to 0.159 showed a moderate level of population differentiations, and Bayesian and clustering analysis consistently supported that these populations could be divided into 7 clusters. This study generated novel microsatellites and new evidence of genetic differentiation between wild and cultured populations of black carp, which are useful for conservation and sustainable utilization of fishery resources.

Genetic Variation May Have Promoted the Successful Colonization of the Invasive Gall Midge, Obolodiplosis robiniae, in China.

Invasive species often cause serious economic and ecological damage. Despite decades of extensive impacts of invasives on bio-diversity and agroforestry, the mechanisms underlying the genetic adaptation and rapid evolution of invading populations remain poorly understood. The black locust gall midge, Obolodiplosis robiniae, a highly invasive species that originated in North America, spread widely throughout Asia and Europe in the past decade. Here, we used 11 microsatellite DNA markers to analyze the genetic variation of 22 O. robiniae populations in China (the introduced region) and two additional US populations (the native region). A relatively high level of genetic diversity was detected among the introduced populations, even though they exhibited lower diversity than the native US populations. Evidence for genetic differentiation among the introduced Chinese populations was also found based on the high Fst value compared to the relatively low among the native US populations. Phylogenetic trees, structure graphical output, and principal coordinate analysis plots suggested that the Chinese O. robiniae populations (separated by up to 2,540 km) cluster into two main groups independent of geographical distance. Genetic variation has been observed to increase rapidly during adaptation to a new environment, possibly contributing to population establishment and spread. Our results provide insights into the genetic mechanisms underlying successful invasion, and identify factors that have contributed to colonization by an economically important pest species in China. In addition, the findings improve our understanding of the role that genetic structure plays during invasion by O. robiniae.

High Connectivity of the White Seabream (Diplodus sargus, L. 1758) in the Aegean Sea, Eastern Mediterranean Basin.

Population dynamics in the marine realm can shape species’ spatial structure and genetic variability between given geographical areas. Connectivity is an important factor of species’ population structure. In this study, we examined the genetic diversity and structure of white seabream (Diplodus sargus, L. 1758) in the eastern Mediterranean basin, using a panel of four microsatellite markers. Recorded low FST values within the study area indicate little evidence of genetic differentiation among populations. Results suggest high gene flow which may imply near-panmixia between populations, indicating the possibility of a probable movement of adult migrants, or strong passive drift at sea in early life stages of the species. To this extent, bibliographically speaking, different species within the Sparidae family favor altered population dynamics patterns with respect to local populations and genetic divergence, in the context of the molecular marker used.

Genotyping-by-Sequencing Reveals Fine-Scale Differentiation in Populations of Pseudoperonospora humuli.

Pseudoperonospora humuli is the causal agent of downy mildew of hop, one of the most important diseases of this plant and a limiting factor for production of susceptible cultivars in certain environments. The degree of genetic diversity and population differentiation within and among P. humuli populations at multiple spatial scales was quantified using genotyping-by-sequencing to test the hypothesis that populations of P. humuli have limited genetic diversity but are differentiated at the scale of individual hop yards. Hierarchical sampling was conducted to collect isolates from three hop yards in Oregon, plants within these yards, and infected shoots within heavily diseased plants. Additional isolates also were collected broadly from other geographic regions and from the two previously described clades of the sister species, P. cubensis. Genotyping of these 240 isolates produced a final quality-filtered data set of 216 isolates possessing 25,227 variants. Plots of G'ST values indicated that the majority of variants had G'ST values near 0 and were scattered randomly across contig positions. However, there was a subset of variants that were highly differentiated (G'ST > 0.3) and reproducible when genotyped independently. Within P. humuli, there was evidence of genetic differentiation at the level of hop yards and plants within yards; 19.8% of the genetic variance was associated with differences among yards and 20.3% of the variance was associated with plants within the yard. Isolates of P. humuli were well differentiated from two isolates of P. cubensis representative of the two clades of this organism. There was strong evidence of linkage disequilibrium in variant loci, consistent with nonrandom assortment of alleles expected from inbreeding and/or asexual recombination. Mantel tests found evidence that the genetic distance between isolates collected from heavily diseased plants within a hop yard was associated with the physical distance of the plants from which the isolates were collected. The sum of the data presented here indicates that populations of P. humuli are consistent with a clonal or highly inbred genetic structure with a small, yet significant differentiation of populations among yards and plants within yards. Fine-scale genetic differentiation at the yard and plant scales may point to persistence of founder genotypes associated with planting material, and chronic, systemic infection of hop plants by P. humuli. More broadly, genotyping-by-sequencing appears to have sufficient resolution to identify rare variants that differentiate subpopulations within organisms with limited genetic variability.

Genetic differentiation between and within ecotypes of pike (Esox lucius) in the Baltic Sea

Abstract Aquatic systems often lack physical boundaries for gene flow, but ecological and behavioural barriers can form surprisingly fine spatial scale genetic patterns that challenge traditional, large scale management. To detect fine spatial scale structures, understand sources of intraspecific diversity, and design appropriate management plans requires identification of reproductively isolated units. This study reports on genetic differentiation in pike (Esox lucius) within a coastal area stretching 55 km from south to north in the central Baltic Sea. Pike is here an economically and ecologically important top predator that has declined in abundance. However, population structures have mostly been studied on large spatial scales, and without considering the potential for genetic divergence between the sympatric anadromous fresh water and the resident brackish water spawning ecotypes. To this end, 487 individuals from the east coast of Sweden and the island of Öland, representing sympatric anadromous and resident spawning individuals, categorized to ecotype based on spawning location or otolith microchemistry, were genotyped for 10 microsatellites and used to test for divergence between ecotypes. Furthermore, divergence between regions (island/mainland), neighbouring spawning locations (n = 13) and isolation by distance within and between regions were evaluated for the anadromous ecotype. The results revealed strong genetic differences between regions, between spawning locations separated by as little as 5 km and the first evidence of genetic differentiation between resident and anadromous ecotypes; despite a high dispersal capacity of pike and a high connectivity within the study area. The signatures of isolation by distance indicated that connectivity among populations differed between regions, probably reflecting availability of spawning habitats. To safeguard against the challenges and uncertainties associated with environmental change, adaptive conservation management should aim to promote high intra‐population functional genetic diversity without compromising the continued integrity and coexistence of the different ecotypes and of locally adapted sub‐populations.

The use of spatially explicit genetic variation data from four deep-sea sponges to inform the protection of Vulnerable Marine Ecosystems

The United Nations General Assembly has called for greater protection of the world’s deep-sea species and of features such as Vulnerable Marine Ecosystems (VMEs). Sponges are important components of VMEs and information about their spatially explicit genetic diversity can inform management decisions concerning the placement of protected areas. We employed a spatially explicit hierarchical testing framework to examine genetic variation amongst archived samples of four deep-sea sponges in the New Zealand region. For Poecillastra laminaris Sollas 1886, significant mitochondrial (COI, Cytb) and nuclear DNA (microsatellite) genetic differences were observed between provinces, amongst north-central-south regions and amongst geomorphic features. For Penares sp. no significant structure was detected (COI, 12S) across the same areas. For both Neoaulaxinia persicum Kelly, 2007 (COI, 12S) and Pleroma menoui Lévi & Lévi 1983 (COI) there was no evidence of genetic differentiation within their northern only regional distributions. Of 10 separate species-by-marker tests for isolation-by-distance and isolation-by-depth, only the isolation-by-depth test for N. persicum for COI was significant. The use of archived samples highlights how historical material may be used to support national and international management decisions. The results are discussed in the broader context of existing marine protected areas, and possible future design of spatial management measures for protecting VMEs in the New Zealand region.