Genetic structure of the Canarian palm tree (Phoenix canariensis) at the island scale: does the ‘island within islands’ concept apply to species with high colonisation ability?

• Oceanic islands are dynamic settings that often promote within‐island patterns of strong population differentiation. Species with high colonisation abilities, however, are less likely to be affected by genetic barriers, but island size may impact on species genetic structure regardless of dispersal ability.
• The aim of the present study was to identify the patterns and factors responsible for the structure of genetic diversity at the island scale in Phoenix canariensis, a palm species with high dispersal potential. To this end, we conducted extensive population sampling on the three Canary Islands where the species is more abundant and assessed patterns of genetic variation at eight microsatellite loci, considering different within‐island scales.
• Our analyses revealed significant genetic structure on each of the three islands analysed, but the patterns and level of structure differed greatly among islands. Thus, genetic differentiation fitted an isolation‐by‐distance pattern on islands with high population densities (La Gomera and Gran Canaria), but such a pattern was not found on Tenerife due to strong isolation between colonised areas. In addition, we found a positive correlation between population geographic isolation and fine‐scale genetic structure.
• This study highlights that island size is not necessarily a factor causing strong population differentiation on large islands, whereas high colonisation ability does not always promote genetic connectivity among neighbouring populations. The spatial distribution of populations (i.e. landscape occupancy) can thus be a more important driver of plant genetic structure than other island, or species′ life‐history attributes.

     

Spatial genetic analysis of two polyploid macrophytes reveals high connectivity in a modified wetland

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Watershed‐level brook trout genetic structuring: Evaluation and application of riverscape genetics models

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Landscape Features Fail to Explain Spatial Genetic Structure in White-Tailed Deer Across Ohio,USA

Landscape features influence wildlife movements across spatial scales and have the potential to influence the spread of disease. Chronic wasting disease (CWD) is a fatal prion disease affecting members of the family Cervidae, particularly white-tailed deer (Odocoileus virginianus), and the first positive CWD case in a wild deer in Ohio, USA, was recorded in 2020. Landscape genetics approaches are increasingly used to better understand potential pathways for CWD spread in white-tailed deer, but little is known about genetic structure of white-tailed deer in Ohio. The objectives of our study were to evaluate spatial genetic structure in white-tailed deer across Ohio and compare the support for isolation by distance (IBD) and isolation by landscape resistance (IBR) models in explaining this structure. We collected genetic data from 619 individual deer from 24 counties across Ohio during 2007–2009. We used microsatellite genotypes from 619 individuals genotyped at 11 loci and haplotypes from a 547-base pair fragment of the mitochondrial DNA control region. We used spatial and non-spatial genetic clustering tests to evaluate genetic structure in both types of genetic data and empirically optimized landscape resistance surfaces to compare IBD and IBR using microsatellite data. Non-spatial genetic clustering tests failed to detect spatial genetic structure, whereas spatial genetic clustering tests indicated subtle spatial genetic structure. The IBD model consistently outperformed IBR models that included land cover, traffic volume, and streams. Our results indicated widespread genetic connectivity of white-tailed deer across Ohio and negligible effects of landscape features. These patterns likely reflect some combination of minimal resistive effects of landscape features on white-tail deer movement in Ohio and the effects of regional recolonization or translocation. We encourage continued CWD surveillance in Ohio, particularly in the proximity of confirmed cases. © 2021 The Wildlife Society. This article has been contributed to by US Government employees and their work is in the public domain in the USA.     

Watershed characteristics shape the landscape genetics of brook stickleback (Culaea inconstans) in shallow prairie lakes

Investigating the consequences of landscape features on population genetic patterns is increasingly important to elucidate the ecological factors governing connectivity between populations and predicting the evolutionary consequences of landscapes. Small prairie lakes in Alberta, Canada, and the brook stickleback (Culaea inconstans) that inhabit them, provide a unique aquatic system whereby populations are highly isolated from one another. These heterogeneous and extreme environments are prone to winterkills, an event whereby most of the fish die and frequent bottlenecks occur. In this study, we characterized the genetic population structure of brook stickleback among several lakes, finding that the species is hierarchically influenced by within‐lake characteristics in small‐scale watersheds. Landscape genetic analyses of the role of spatial features found support for basin characteristics associated with genetic diversity and bottlenecks in 20% of the sampled lakes. These results suggest that brook stickleback population genetic patterns may be driven, at least in part, by ecological processes that accelerate genetic drift and landscape patterns associated with reduced dispersal. Collectively, these results reinforce the potential importance of connectivity in the maintenance of genetic diversity, especially in fragmented landscapes.     

Spatial extent of analysis influences observed patterns of population genetic structure in a widespread darter species (Percidae)

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A genomic assessment of population structure and gene flow in an aquatic salamander identifies the roles of spatial scale,barriers, and river architecture

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Urban population genetics of slum‐dwelling rats (Rattus norvegicus) in Salvador,Brazil

Throughout the developing world, urban centres with sprawling slum settlements are rapidly expanding and invading previously forested ecosystems. Slum communities are characterized by untended refuse, open sewers and overgrown vegetation, which promote rodent infestation. Norway rats (Rattus norvegicus) are reservoirs for epidemic transmission of many zoonotic pathogens of public health importance. Understanding the population ecology of R. norvegicus is essential to formulate effective rodent control strategies, as this knowledge aids estimation of the temporal stability and spatial connectivity of populations. We screened for genetic variation, characterized the population genetic structure and evaluated the extent and patterns of gene flow in the urban landscape using 17 microsatellite loci in 146 rats from nine sites in the city of Salvador, Brazil. These sites were divided between three neighbourhoods within the city spaced an average of 2.7 km apart. Surprisingly, we detected very little relatedness among animals trapped at the same site and found high levels of genetic diversity, as well as structuring across small geographical distances. Most F_ST comparisons among sites were statistically significant, including sites <400 m apart. Bayesian analyses grouped the samples in three genetic clusters, each associated with distinct sampling sites from different neighbourhoods or valleys within neighbourhoods. These data indicate the existence of complex genetic structure in R. norvegicus in Salvador, linked to the heterogeneous urban landscape. Future rodent control measures need to take into account the spatial and temporal linkage of rat populations in Salvador, as revealed by genetic data, to develop informed eradication strategies.     

Spatial differences in genetic diversity and northward migration suggest genetic erosion along the boreal caribou southern range limit and continued range retraction

With increasing human activities and associated landscape changes, distributions of terrestrial mammals become fragmented. These changes in distribution are often associated with reduced population sizes and loss of genetic connectivity and diversity (i.e., genetic erosion) which may further diminish a species' ability to respond to changing environmental conditions and lead to local population extinctions. We studied threatened boreal caribou (Rangifer tarandus caribou) populations across their distribution in Ontario/Manitoba (Canada) to assess changes in genetic diversity and connectivity in areas of high and low anthropogenic activity. Using data from >1,000 caribou and nine microsatellite loci, we assessed population genetic structure, genetic diversity, and recent migration rates using a combination of network and population genetic analyses. We used Bayesian clustering analyses to identify population genetic structure and explored spatial and temporal variation in those patterns by assembling networks based on R_ST and F_ST as historical and contemporary genetic edge distances, respectively. The Bayesian clustering analyses identified broad‐scale patterns of genetic structure and closely aligned with the R_ST network. The F_ST network revealed substantial contemporary genetic differentiation, particularly in areas presenting contemporary anthropogenic disturbances and habitat fragmentation. In general, relatively lower genetic diversity and greater genetic differentiation were detected along the southern range limit, differing from areas in the northern parts of the distribution. Moreover, estimation of migration rates suggested a northward movement of animals away from the southern range limit. The patterns of genetic erosion revealed in our study suggest ongoing range retraction of boreal caribou in central Canada.     

Effects of dams and their environmental impacts on the genetic diversity and connectivity of freshwater mussel populations in Poyang Lake Basin,China

1. Habitat fragmentation is one of the main threats to biodiversity. Barriers to dispersal caused by anthropogenic habitat alteration may affect phylogeographic patterns in freshwater mussels. Knowledge of the phylogenetic and phylogeographic patterns of unionoids is vital to inform protection of their biodiversity.
2. Here, we assessed influences of dams and their environmental effects on the genetic diversity and population connectivity of a broadly distributed freshwater mussel, Nodularia douglasiae, in Poyang Lake Basin.
3. The results showed high genetic diversity in areas without dams and low genetic diversity in areas with dams. High genetic differentiation and low gene flow were found among the 11 populations. Genetic variation was significantly correlated with dissolved oxygen levels.
4. The observation of low genetic diversity in populations separated by dams indicated that those populations were subjected to genetic erosion and demographic decline because they are disconnected from other populations with higher diversity. High genetic differentiation and low gene flow among the 11 populations could be correlated with anthropogenic habitat alteration.
5. These results indicated that anthropogenic habitat alterations have led to the decline in freshwater mussel diversity. Therefore, we recommend maintaining favourable habitat conditions and connectivity of rivers or lakes, and strengthening study of life histories with host-test experiments to identify potential host fish species to strengthen the knowledge base underpinning freshwater mussel conservation.

     

Landscape features impact connectivity between soil populations: a comparative study of gene flow in earthworms

Landscape features are known to alter the spatial genetic variation of aboveground organisms. Here, we tested the hypothesis that the genetic structure of belowground organisms also responds to landscape structure. Microsatellite markers were used to carry out a landscape genetic study of two endogeic earthworm species, Allolobophora chlorotica (N = 440, eight microsatellites) and Aporrectodea icterica (N = 519, seven microsatellites), in an agricultural landscape in the North of France, where landscape features were characterized with high accuracy. We found that habitat fragmentation impacted genetic variation of earthworm populations at the local scale. A significant relationship was observed between genetic diversity (H_e, A_r) and several landscape features in A. icterica populations and A. chlorotica. Moreover, a strong genetic differentiation between sites was observed in both species, with a low degree of genetic admixture and high F_st values. The landscape connectivity analysis at the regional scale, including isolation by distance, least‐cost path and cost‐weighted distance approaches, showed that genetic distances were linked to landscape connectivity in A. chlorotica. This indicates that the fragmentation of natural habitats has shaped their dispersal patterns and local effective population sizes. Landscape connectivity analysis confirmed that a priori favourable habitats such as grasslands may constitute dispersal corridors for these species.     

Comparative landscape genetics of pond‐breeding amphibians in Mediterranean temporal wetlands: The positive role of structural heterogeneity in promoting gene flow

Comparative landscape genetics studies can provide key information to implement cost‐effective conservation measures favouring a broad set of taxa. These studies are scarce, particularly in Mediterranean areas, which include diverse but threatened biological communities. Here, we focus on Mediterranean wetlands in central Iberia and perform a multi‐level, comparative study of two endemic pond‐breeding amphibians, a salamander (Pleurodeles waltl) and a toad (Pelobates cultripes). We genotyped 411 salamanders from 20 populations and 306 toads from 16 populations at 18 and 16 microsatellite loci, respectively, and identified major factors associated with population connectivity through the analysis of three sets of variables potentially affecting gene flow at increasingly finer levels of spatial resolution. Topographic, land use/cover, and remotely sensed vegetation/moisture indices were used to derive optimized resistance surfaces for the two species. We found contrasting patterns of genetic structure, with stronger, finer scale genetic differentiation in Pleurodeles waltl, and notable differences in the role of fine‐scale patterns of heterogeneity in vegetation cover and water content in shaping patterns of regional genetic structure in the two species. Overall, our results suggest a positive role of structural heterogeneity in population connectivity in pond‐breeding amphibians, with habitat patches of Mediterranean scrubland and open oak woodlands (“dehesas”) facilitating gene flow. Our study highlights the usefulness of remotely sensed continuous variables of land cover, vegetation and water content (e.g., NDVI, NDMI) in conservation‐oriented studies aimed at identifying major drivers of population connectivity.     

Lasting through the ice age: The role of the proglacial refugia in the maintenance of genetic diversity,population growth,and high dispersal rate in a widespread freshwater crustacean

1. The severe climatic changes during the Pleistocene ice ages have shaped the genetic structure and distribution of biota in Europe. We aimed to reveal in detail the genetic diversity, geographical population structure, historical and present demography, migration patterns, and the presence of possible glacial refugia within the nominative subspecies Asellus aquaticus aquaticus.
2. We analysed DNA sequences of the mitochondrial cytochrome c oxidase subunit I gene and nuclear noncoding internal transcribed spacer II region, from populations inhabiting post-glacial Europe (from the British Isles and Scandinavia to the northern Mediterranean and Black Sea coasts).
3. The origin of the taxon, including establishment in the Dinaric Western Balkans, dates to the Middle/Late Pliocene, but most of its genetic diversity emerged during the Middle/Late Pleistocene before the Last Glacial Maximum.
4. Despite the general absence of spatial genetic structure with population growth, we discovered two different phylogeographic stories across 11 clusters revealed by a coalescent approach. Firstly, the periglacial cluster group—spatially restricted mainly to the northern Balkans, Pannonian Basin, and Pontic Region—is older and more divergent. It apparently retained a relatively stable population size during the glacial-interglacial cycles. Conversely, the proglacial cluster group—widely distributed in areas close to the glacier margins (north of the Alps, Sudetes, Carpathians) and in the Pannonian Basin—is younger and composed of closely related individuals. It originated in Pleistocene and lasted continuously through the Last Glacial Maximum in numerous high latitude refugia. This was probably due to the vast network of proglacial lakes and rivers, which played a crucial role in the maintenance of genetic diversity, population growth, and high dispersal rate.
5. The evolutionary history of A. a. aquaticus reveals unexpected patterns and is an important lesson when making predictions for other aquatic taxa. Our results suggest that we should stop perceiving the proglacial habitats as lifeless ice desert.

     

Environmental gradients shape the genetic structure of two medicinal Salvia species in Jordan

• Environmental gradients, and particularly climatic variables, exert a strong influence on plant distribution and, potentially, population genetic diversity and differentiation. Differences in water availability can cause among‐population variation in ecological processes and can thus interrupt populations’ connectivity and isolate them environmentally. The present study examines the effect of environmental heterogeneity on plant populations due to environmental isolation unrelated to geographic distance.
• Using AFLP markers, we analyzed genetic diversity and differentiation among 12 Salvia spinosa populations and 13 Salvia syriaca populations from three phytogeographical regions (Mediterranean, Irano‐Turanian and Saharo‐Arabian) representing the extent of the species’ geographic range in Jordan. Differences in geographic location and climate were considered in the analyses.
• For both species, flowering phenology varied among populations and regions. Irano‐Turanian and Saharo‐Arabian populations had higher genetic diversity than Mediterranean populations, and genetic diversity increased significantly with increasing temperature. Genetic diversity in Salvia syriaca was affected by population size, while genetic diversity responded to drought in S. spinosa. For both species, high levels of genetic differentiation were found as well as two well‐supported phytogeographical groups of populations, with Mediterranean populations clustering in one group and the Irano‐Turanian and Saharo‐Arabian populations in another. Genetic distance was significantly correlated to environmental distance, but not to geographic distance.
• Our data indicate that populations from moist vs. arid environments are environmentally isolated, where environmental gradients affect their flowering phenology, limit gene flow and shape their genetic structure. We conclude that environmental heterogeneity may act as driver for the observed variation in genetic diversity.

     

Aquatic insects in a sea of desert: population genetic structure is shaped by limited dispersal in a naturally fragmented landscape

Habitat requirements and landscape features can exert strong influences on the population structure of organisms. For aquatic organisms in particular, hydrologic requirements can dictate the extent of available habitat, and thus the degree of genetic connectivity among populations. We used a landscape genetics approach to evaluate hypotheses regarding the influence of landscape features on connectivity among populations of the giant water bug Abedus herberti (Hemiptera: Belostomatidae). Abedus herberti is restricted to naturally‐fragmented, perennial stream habitats in arid regions of North America. This species is exceptional because it is flightless at all life stages. Thus, we hypothesized a high degree of population genetic structure in A. herberti due to hydrologic constraints on habitat and low dispersal ability of the organism. A total of 617 individuals were sampled from 20 populations across southeastern Arizona, USA and genotyped at 10 microsatellite loci. We used a Bayesian clustering method to delineate genetic groups among populations. To determine which of six landscape variables (representing hypotheses of landscape‐level connectivity) has the strongest association with genetic connectivity in A. herberti, we used information‐theoretic model selection. Strong population structure was evident among A. herberti populations, even at small spatial scales. At a larger scale, A. herberti populations were hierarchically structured across the study region, with groups of related populations generally occurring in the same mountain range, rather than in the same major watershed. Surprisingly, stream network connectivity was not important for explaining among‐population patterns. Only the Curvature landscape variable was identified as having an association with genetic connectivity in A. herberti. The Curvature variable hypothesizes that gene flow tends to occur where local topography is concave, such as within stream drainages and dry gullies. Thus, our results suggest that population connectivity may depend on the shape of local overland topography rather than direct connectivity within stream drainage networks.     

Differential effects of spatial network structure and scale on population size and genetic diversity of the ninespine stickleback in a remnant wetland system

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Effect of the landscape matrix on gene flow in a coastal amphibian metapopulation

Functional connectivity is crucial for the persistence of a metapopulation, because migration among subpopulations enables recolonization and counteracts genetic drift, which is especially important in small subpopulations. We studied the degree and drivers of connectivity among occupied patches of a coastal dune metapopulation of the Natterjack Toad (Epidalea calamita Laurenti), on the basis of microsatellite variation. As spatial landscape heterogeneity is expected to influence dispersal and genetic structure, we analyzed which landscape features affect functional connectivity and to what extent. Sixty different landscape resistance scenarios as well as the isolation-by-distance model were compared using two landscape genetics approaches. We identified three subpopulations with unidirectional levels of gene flow among the two most geographically separated subpopulations, while inferred gene flow into the geographically intermediate subpopulation was limited. Urbanization and vegetation height negatively affected connectivity. Low estimates of genetic diversity and effective population size indicate that conservation measures in the smallest and most isolated subpopulation are required.     

Agricultural intensification alters marbled newt genetic diversity and gene flow through density and dispersal reduction

Recent agricultural intensification threatens global biodiversity with amphibians being one of the most impacted groups. Because of their biphasic life cycle, amphibians are particularly vulnerable to habitat loss and fragmentation that often result in small, isolated populations and loss of genetic diversity. Here, we studied how landscape heterogeneity affects genetic diversity, gene flow and demographic parameters in the marbled newt, Triturus marmoratus, over a hedgerow network landscape in Western France. While the northern part of the study area consists of preserved hedged farmland, the southern part was more profoundly converted for intensive arable crops production after WWII. Based on 67 sampled ponds and 10 microsatellite loci, we characterized regional population genetic structure and evaluated the correlation between landscape variables and (i) local genetic diversity using mixed models and (ii) genetic distance using multiple regression methods and commonality analysis. We identified a single genetic population characterized by a spatially heterogeneous isolation-by-distance pattern. Pond density in the surrounding landscape positively affected local genetic diversity while arable crop land cover negatively affected gene flow and connectivity. We used demographic inferences to quantitatively assess differences in effective population density and dispersal between the contrasted landscapes characterizing the northern and southern parts of the study area. Altogether, results suggest recent land conversion affected T. marmoratus through reduction in both effective population density and dispersal due to habitat loss and reduced connectivity.     

Migratory behaviour shapes spatial genetic structure of cyprinid fishes within the Lake Malawi catchment

• Genetic differences among freshwater fish populations are dependent on life‐history characteristics of the species, including the range of adult dispersal and the extent of homing to natal breeding grounds. However, the effects of variation in such characteristics on population genetic connectivity are rarely studied comparatively among closely related species.
• We studied population genetic structure within three congeneric cyprinid species from the Lake Malawi catchment that differ substantially in life‐history traits and conservation status, using a combination of microsatellite and mitochondrial DNA markers. Mpasa (Opsaridium microlepis) is a large (70 cm total length) migratory species that spawns in rivers, but as an adult is exclusively known from the main lake body. Sanjika (Opsaridium microcephalum), is a medium size (30 cm total length) species that exists in lake breeding, river‐lake migratory and apparently landlocked populations. Dwarf sanjika (Opsaridium tweddleorum) is a small non‐migratory species (15 cm total length) that persists in small tributaries surrounding the main lake and adjoining rivers.
• The results revealed striking differences among the three species in spatial genetic structuring. The river‐lake migratory mpasa showed only weak yet significant population genetic structure within the main Lake Malawi catchment, suggesting that there is no strong natal homing. The habitat‐generalist sanjika showed only weak spatial genetic differentiation at microsatellite loci within the Lake Malawi catchment, but moderate structure in mitochondrial DNA, potentially reflecting male‐biased dispersal. The river‐restricted dwarf sanjika showed strong genetic structure in both microsatellite and mitochondrial DNA, suggesting strictly limited dispersal at both adult and juvenile stages.
• We conclude that contrasting migration life histories have resulted in dramatically different patterns of population genetic structure among these congeneric species. The observed patterns demonstrate how divergent life‐history evolution may strongly influence broader patterns of population genetic connectivity in freshwater fish, with consequences for management and conservation. Specifically the results suggesting gene flow among Lake Malawi populations of mpasa, an IUCN red‐listed ‘Endangered’ species endemic to the lake catchment, imply that conservation initiatives operating at both local and catchment scales are needed to reverse local population decline.