Landscape location affects genetic variation of Canada lynx (Lynx canadensis)

The effect of a population's location on the landscape on genetic variation has been of interest to population genetics for more than half a century. However, most studies do not consider broadscale biogeography when interpreting genetic data. In this study, we propose an operational definition of a peripheral population, and then explore whether peripheral populations of Canada lynx (Lynx canadensis) have less genetic variation than core populations at nine microsatellite loci. We show that peripheral populations of lynx have fewer mean numbers of alleles per population and lower expected heterozygosity. This is surprising, given the lynx's capacity to move long distances, but can be explained by the fact that peripheral populations often have smaller population sizes, limited opportunities for genetic exchange and may be disproportionately affected by ebbs and flows of species' geographical range.     

Simulating the dispersal of hemlock woolly adelgid in the temperate forest understory

The hemlock woolly adelgid (HWA), Adelges tsugae Annand (Hemiptera: Adelgidae), has spread rapidly across the eastern USA since its introduction from Japan 60 years ago, causing widespread mortality of both eastern hemlock [Tsuga canadensis (L.) Carrière] and Carolina hemlock [Tsuga caroliniana Engelm. (Pinaceae)]. Although HWA spread patterns have been repeatedly analyzed at regional scales, comparatively little is known about its dispersal potential within and between hemlock stands. As the small size and clonal nature of HWA make it nearly impossible to identify the source populations of dispersing individuals, we simulated intra‐stand HWA movement in the field by monitoring the movement of clumps of fluorescent powder that are slightly larger than HWA, but much easier to detect in the forest understory. Using three hemlock trees with three colors of fluorescent powder as source populations, we detected dispersal events at the farthest distances within our trapping array (400 m). However, more than 90% of dispersal events were <25 m. Dispersal patterns were similar from all three source trees and the distribution of dispersal distances in all cases could be described by lognormal probability density functions with mean dispersal distance of 12–14 m, suggesting that dispersal was relatively independent of location of source trees. In general, we documented tens of thousands of passive dispersal events in the forest understory despite the presence of a dense forest canopy. Thus, even under relatively light‐wind conditions, particles of similar dimensions to HWA are capable of intra‐stand movement, suggesting that a large population of HWA could rapidly infest other trees within several hundred meter radius, or beyond.     

Population structure and mitochondrial DNA variation in sedentary Neotropical birds isolated by forest fragmentation

The current worldwide concern about tropical deforestation raises questions about the sustainability of avian populations in isolated forest fragments. One of the most important issues concerns the sizes of forest fragments necessary to maintain populations and the genetic variation within them. We address this by: (1) using mtDNA sequence variation to infer aspects of the population structure of four species of understory birds from four sites in southern Costa Rican rainforest; and (2) determining whether forest fragmentation that has occurred in the last 50 years has had an effect on the amount of within-population variation for the species in question. High levels of between-population differentiation (D _xy ) were found over a relatively small geographic scale (<130 km) for white-breasted wood-wren (Henicorhina leucosticta), bicolored antbird (Gymnopithys leucaspis), and gray-headed tanager (Eucometis penicillata), suggesting that these species are highly sedentary and exhibit strong female philopatry. No mtDNA variation was found in Plain Antvireo (Dysithamnus mentalis). In all three of the polymorphic species there was a significant decrease in mtDNA nucleotide diversity in populations isolated by forest fragmentation as compared to populations in contiguous primary forest. Even in relatively large (250–1000 ha) forest reserves, sedentary avian species have lost roughly half (range 43–85) of the nucleotide diversity in mtDNA over a relatively short period of time. Our results indicate that sedentary avian species in forest fragments isolated by clearing have undergone severe reductions in effective population size due to population bottlenecks perpetuated by prolonged isolation and potential edge effects.     

Effect of root competition and shading on growth of suppressed western hemlock (Tsuga heterophylla)

Factors suppressing the growth of Tsuga heterophylla, western hemlock, (40–200 cm tall) were separated into aboveground and belowground components. Canopy manipulation by creating gaps produced approximately a 30–34% increase in the overall amount of light available. Growth of the previously suppressed T. heterophylla was increased by minimizing root competition by trenching around individuals and to a much lesser degree by altering the canopy. The combination of the two manipulations did now show a strong synergistic effect.I thank Greg Helve and Randy Kelley for digging trenches. R. Mack, J. Thompson, J. Franklin, and A. McKee provided useful suggestions throughout the study. I appreciate the comments from the Ecological Discussion Group at Washington State University. This study was supported partially with funds to Oregon State University from the National Science Foundation, as well as the Society of Sigma Xi, and Washington State University.     

Widespread inbreeding and unexpected geographic patterns of genetic variation in eastern hemlock (Tsuga canadensis), an imperiled North American conifer

Eastern hemlock (Tsuga canadensis [L.] Carr.) is an ecologically important tree species experiencing severe mortality across much of its eastern North American distribution, caused by infestation of the exotic hemlock woolly adelgid (Adelges tsugae Annand). To guide gene conservation strategies for this imperiled conifer, we conducted a range-wide genetic variation study for eastern hemlock, amplifying 13 highly polymorphic nuclear microsatellite loci in 1,180 trees across 60 populations. The results demonstrate that eastern hemlock exhibits moderate inbreeding, possibly a signature of a prehistoric decline associated with a widespread insect outbreak. Contrary to expectations, populations in formerly glaciated regions are not less genetically diverse than in the putative southern refugial region. As expected, peripheral disjunct populations are less genetically diverse than main-range populations, but some are highly genetically differentiated or contain unique alleles. Spatially explicit Bayesian clustering analyses suggest that three or four Pleistocene glacial refuges may have existed in the Southeastern United States, with a main post-glacial movement into the Northeast and the Great Lakes region. Efforts to conserve eastern hemlock genetic material should emphasize the capture of broad adaptability that occurs across the geographic range of the species, as well as genetic variability within regions with the highest allelic richness and heterozygosity, such as the Southern Appalachians and New England, and within disjunct populations that are genetically distinct. Much genetic variation exists in areas both infested and uninfested by the adelgid.     

Four centuries of forest clearance and regeneration in the hinterland of a large city

In the last 350 years, forests of eastern North America have experienced widespread clearance and regrowth with local variation in timing and extent determined by patterns of human land use. This paper describes the history of forest in the hinterland of a large city (Wilmington, Delaware) surrounded by fertile soils and having access to a navigable estuary. Forests were cleared between 1650 and 1780 to accommodate shifting cultivation of cereal crops and to provide fuelwood for nearby cities. Proximity to urban markets supported a vigorous agricultural economy through the 19th century and delayed widespread forest regeneration. Reforestation began on a large scale following the local decline of agriculture 1920–1940. In the late 20th century, forest competes for land with suburban housing. Although a similar sequence has occurred throughout eastern North America, the study area is unique in that a larger proportion of original forest was cleared and reforestation began much later than in other regions. Today, the history of land use is evident in the high proportion of young, successional forest and the very small area of long-established forest.     

Rapid,pervasive genetic differentiation of urban white‐footed mouse (Peromyscus leucopus) populations in New York City

We investigated genetic diversity and structure of urban white‐footed mouse, Peromyscus leucopus, populations in New York City (NYC) using variation at 18 microsatellite loci. White‐footed mice are ‘urban adapters’ that occur at higher population densities as habitat fragments are reduced in area but have a limited ability to disperse through urbanized areas. We hypothesized that this combination of traits has produced substantial genetic structure but minimal loss of genetic variation over the last century in NYC. Allelic diversity and heterozygosity in 14 NYC populations were high, and nearly all of our NYC study sites contained genetically distinct populations of white‐footed mice as measured by pairwise F_ST, assignment tests, and Bayesian clustering analyses performed by Structure and baps . Analysis of molecular variance revealed that genetic differences between populations separated by a few kilometres are more significant than differences between prehistorically isolated landmasses (i.e. Bronx, Queens, and Manhattan). Allele size permutation tests and lack of isolation by distance indicated that mutation and migration are less important than drift as explanations for structure in urban, fragmented P. leucopus populations. Peromyscus often exhibit little genetic structure over even regional scales, prompting us to conclude that urbanization is a particularly potent driver of genetic differentiation compared to natural fragmentation.     

Geographic patterns of genetic diversity in Poulsenia armata (Moraceae): implications for the theory of Pleistocene refugia and the importance of riparian forest

Abstract. Tropical forests are species-diverse communities, but we know very little about the geographical distribution of genetic diversity within a species. During the late Pleistocene, lower temperatures and rainfall reduced the distribution of tropical wet forests, and in Central America lowland species may have been limited to riparian habitats. Approximately 12,000 years bp , temperature and rainfall increased in Central America, the distribution of wet forest species expanded, and today the distribution of some species extends into southern Mexico. The distribution of genetic diversity, based on RAPD markers, among ten populations of Poulsenia armata (Miq.) Standl. (Moraceae) suggests that these populations did not originate from a single refugium or region in the late Pleistocene. The Central American populations had high genetic diversity and unique bands giving support to the hypothesis that populations of P. armata occurred in Central American during the late Pleistocene. The majority of genetic diversity was partitioned among populations and there was no geographical relationship among populations, suggesting that these populations were isolated for a long period and there has been little gene flow. Populations of P. armata may have persisted in riparian zones along the Caribbean coast during the late Pleistocene. Given that riparian forest can support high levels of biodiversity in ecological time, and they have played an important role during periods of climate change over geological time, their conservation is of utmost importance particularly with the threat of a rapid shift in climatic patterns.     

Persistence of British natterjack toad Bufo calamita Laurenti (Anura: Bufonidae) populations despite low genetic diversity

Like other amphibians native to Britain, the natterjack toad Bufo calamita must have colonized the islands during the relatively short period between the end of the last glaciation and the separation of Britain from mainland Europe by rising sea levels. Unlike the other native amphibians, however, B. calamita is a habitat specialist at the north-westerly edge of its biogeographical range and for most of the 8000–10000 years since its colonization has probably been restricted to open dunes, heathlands and upper saltmarshes, as isolated populations in a few discrete areas of the country. We have investigated the genetic diversity and relatedness of six widely separated British natterjack populations by allozyme analysis, and shown that all have very low diversity (Overall P _95%= 2.7%, H = 0.004) by comparison with other anurans, including natterjack populations in mainland Europe and common frogs ( Rana temporaria , L) in Britain. Eighty percent of loci were fixed for the same allele in all six British natterjack populations and genetic differentiation between colonies was extremely low. The possible significance of these findings to the persistence of small isolated populations at range edges is discussed.     

High levels of variation despite genetic fragmentation in populations of the endangered mountain pygmy-possum, Burramys parvus, in alpine Australia

In endangered mammals, levels of genetic variation are often low and this is accompanied by genetic divergence among populations. The mountain pygmy-possum (Burramys parvus) is an endangered marsupial restricted to the alpine region of Victoria and New South Wales, Australia. By scoring variation at eight microsatellite loci, we found that B. parvus populations exhibit high levels of genetic divergence and fall into three distinct groups from the northern, central and southern areas of the distribution of this species, consistent with previous assessments of mitochondrial DNA variation. F(ST) values between populations from these regions ranged from 0.19 to 0.54. Within the central area, there was further genetic fragmentation, and a linear association between genetic and geographical distance. This pattern is likely to reflect limited dispersal across barriers despite the fact that individual B. parvus can move several kilometres. Levels of genetic variation within populations were high with the exception of a southern population where there was evidence of inbreeding. From a conservation perspective, all three areas where B. parvus are found should be considered as separate gene pools; management of populations within these areas needs to take into account the low gene flow between populations, as well as threats posed by roads, resorts and other developments in the alpine region. The low genetic variability and inbreeding in the southern population is of particular concern given the high levels of variability in other B. parvus populations.     

Fitness and physiology of Adelges tsugae (Hemiptera: Adelgidae) in relation to the health of the eastern hemlock

The hemlock woolly adelgid, Adelges tsugae Annand is an invasive insect that frequently causes hemlock (Tsuga spp.) mortality in the eastern United States. Studies have shown that once healthy hemlocks become infested by the adelgid, nutrients are depleted from the tree, leading to both tree decline and a reduction of the adelgid population. Since A. tsugae is dependent on hemlock for nutrients, feeding on trees in poor health may affect the ability of the insect to obtain necessary nutrients and may consequently affect their physiological and population health. Trees were categorized as lightly or moderately impacted by A. tsugae based on quantitative and qualitative tree health measurements. Population health of A. tsugae on each tree was determined by measuring insect density and peak mean fecundity; A. tsugae physiological health was determined by measuring insect biomass, total carbon, carbohydrate, total nitrogen, and amino nitrogen levels. Adelges tsugae from moderately impacted trees exhibited significantly greater fecundity than from lightly impacted trees. However, A. tsugae from lightly impacted hemlocks contained significantly greater levels of carbohydrates, total nitrogen, and amino nitrogen. While the results of the physiological analysis generally support our hypothesis that A. tsugae on lightly impacted trees are healthier than those on moderately impacted trees, this was not reflected in the population health measurements. Adelges tsugae egg health in response to tree health should be verified. This study provides the first examination of A. tsugae physiological health in relation to standard A. tsugae population health measures on hemlocks of different health levels.     

Microsatellite analysis of genetic variation in black bear populations

Measuring levels of genetic variation is an important aspect of conservation genetics The informativeness of such measurements is related to the variability of the genetic markers used; a particular concern in species, such as bears, which are characterized by low levels of genetic variation resulting from low population densities and small effective population sizes We describe the development of microsatellite analysis in bears and its use in assessing interpopulation differences in genetic variation in black bears from three Canadian National Parks These markers are highly variable and allowed identification of dramatic differences in both distribution and amount of variation between populations Low levels of variation were observed in a population from the Island of Newfoundland The significance of interpopulation differences in variability was tested using a likelihood ratio test of estimates of θ= 4 N_eu.     

Land use and forest habitat distribution in the hinterland of(r)a large city

The cumulative effect of many local forest disturbances can be estimated from an analysis of forest distribution at the scale of the entire landscape. To gauge the regional impact of forest clearance and regeneration, a history of forest cover was compiled for the twentieth century in the hinterland of a large city (Wilmington, Delaware, U.S.A.). Forest distribution and character were described by point sampling of historical aerial photographs. Environmental features were measured on visits to sample points in the field. Regional forest coverage has grown from c . 5% in 1890 to 22% in 1990. Most modern stands are <60 years old; only 2.5% of the modern landscape is in forest more than 100 years old. Since 1890, patterns of clearance and regeneration have caused a proportional shift in forest cover from uplands to lowlands and flood plains. Older stands are found on rock fields and steep slopes, indicating abandonment from agriculture according to the quality of local sites. Residential development has been concentrated in uplands, precluding regeneration of forest in that landscape position. In general, land use turnover reflects the character of the local site; there is no evidence of region-wide gradients of regeneration or clearance. Modern forest is concentrated along steep-sided stream valleys and away from roads. The great majority of forest lies within 50 m of a forest margin placing it in the microclimatic and vegetational edge zone. Although most forest is within 200 m of a residence, pedestrian traffic appears to have had only a minor impact in the biological community. By contrast, widespread species impoverish- ment is suggested by the overwhelming youthfulness of modern forest and the low degree of connectedness of forest within the landscape. Management for biological conservation should focus on protection of remnant primary forest, rather than relying on succession to restock secondary stands.     

Farming for bees: annual variation in pollinator populations across agricultural landscapes

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Genetic changes associated to declining populations of Formica ants in fragmented forest landscape

We monitored populations of two wood ant species, Formica aquilonia and Formica lugubris, through annual mapping of the colonies in a fragmenting forest landscape from 1966 to 1998. The genetic population structure was studied at the end of the study period by using 12 microsatellite loci. Fragmentation of forest led to a decline and spatial redistribution of populations. Changes in the spatial distribution were particularly pronounced in the highly polygynous (many queens in a single nest) species F. aquilonia, whose local populations declined or became extinct, or relocated themselves and colonized new patches. The genetic relationships of the remaining subpopulations indicated the historical developments, revealing the boundaries of the historical populations (high values of genetic differentiation, F(ST)), recolonization histories (genetic affinities revealed by Bayesian analyses) and population decline (reduced variation). Big genetic differences could be detected over short distances, so differentiation also depended on social factors. Our results showed that a genetic study can be reliably used to dissect the recent historical changes underlying the present population structure, and that species with different social structures can respond differently to habitat changes. Combining our demographic and genetic results suggests that habitat fragmentation forms a clear threat on a local scale with large negative effects on ant population viability.     

Contrasting allozyme and RAPD variation in spider populations from patchy forest habitats

During the last 1000 years, massive deforestation events have occurred in Flanders (the northern part of Belgium) and the remaining forests have become very isolated patches. It is expected that organisms bound to these patchy forest habitats and with limited dispersal capacities will likely experience strong effects of genetic drift. One such organism is the spider Coelotes terrestris. Allozyme data suggested that 10 Flemish populations of this spider showed little genetic variation, as only one out of 20 loci was polymorphic (phosphoglucose isomerase). In view of this result, we used random amplified polymorphic DNA (RAPD) markers to test whether this lack of allozyme diversity is an inherent feature of the populations and/or species studied or whether it rather reflects a characteristic of the markers and/or methods used. Since the RAPD data revealed a substantial amount of genetic diversity in the same 10 populations, our results suggest that the latter is true. Furthermore, the RAPD data agree with the expectations for an organism with low dispersal capacities that has lived in isolated forest patches for at least 200 generations. Supplemented with the results of other techniques and studies, these findings might be of importance for the future conservation of this spider species in Flanders.     

Molecular pilot study on peripheral populations of Kenyan greenbul in an afromontane fragmented forest

We provide a molecular study on peripheral populations of three closely related species of African forest‐dependent greenbuls: the generalist Eurillas latirostris and the specialists Phyllastrephus cabanisi and Arizelocichla nigriceps. These species co‐occur within their range limits in the Kenyan Afromontane forest, Cherangani Hills. This forest has experienced drastic deforestation, which began about 50 years ago, that is causing habitat fragmentation. The aims of this study, using the analyses of molecular tools, are twofold: (i) to provide evidence that functional traits (i.e., ecological attributes) may shape different genetic structure in peripheral populations and (ii) to identify the possible effects of forest fragmentation. Blood and plucked feathers were sampled from a total of 124 birds analysed using two molecular approaches: (i) sequencing of cytochrome b mtDNA and (ii) genotyping nuclear DNA at eight microsatellite loci. Molecular diversity indices, minimum spanning network and mismatch distribution analysis of mtDNA results indicated that the peripheral populations showed different demographic trends: a highly variable and bimodal pattern in forest specialist P. cabanisi, a less variable and unimodal pattern in forest generalist E. latirostris and in the montane specialist A. nigriceps. Although this is a pilot study on the Cherangani forest fragmentation, the nuclear results may not exclude the hypothesis of reduced connectivity in all forest‐dependent greenbuls.