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68 results for “landscape history”
Data from: A model for non-equilibrium metapopulation dynamics utilizing data on species occupancy, patch ages and landscape history
1. The distribution pattern of many species reflects the past rather than the current structure of landscapes. Consequently, species are most often not in equilibrium with the current landscape structure. Yet this is a well-known fact, there is no appropriate approach to estimate the colonization rate of non-equilibrium species based on only data on the species occurrence pattern in the landscape. 2. We present an approach to estimate the colonization rate of non-equilibrium metapopulations. The approach requires only data on species presence/absence among its patches (occurrence pattern), data on patch ages and data on the historic distribution of the patches in the landscape. By estimating the past occurrence patterns and colonization events leading to the current pattern of occupied and non-occupied patches, we estimate the colonization rate, including the dispersal kernel. We also show how to estimate effects of local patch conditions and how to include an independent estimate of the local extinction rate based on other data. We use nine epiphytic lichen species confined to beech trees to illustrate the method. 3. Five species had restricted dispersal range, between 200 and 4700 m, and their colonization rate decreased with increasing fragmentation. Species colonization rates were related to niche width. Among the demographic parameters, the force of colonization was more important than the dispersal range in explaining the colonization rates. Local patch conditions did not explain the colonization probability of any species. In metapopulation projections that did not account for restricted dispersal range, higher future metapopulation sizes were projected. 4. Synthesis. The presented approach uses data on only species occurrence, patch age and landscape history to estimate the species colonization rate and dispersal kernel. It can also utilize independent data on local extinction rate. Rather than identifying factors explaining the occurrence pattern, the model estimates the rate of change in the occurrence pattern. This dynamic modelling allows testing general and applied questions on the dynamics or viability of metapopulations of sessile species. The approach is applicable for species whose distribution pattern reflects the past rather than the current landscape structure, e.g. certain epiphytes and ground-floor plants.
Data from: Landscape history confounds the ability of the NDVI to detect fine-scale variation in grassland communities
1. The NDVI is a remotely-sensed vegetation index that is frequently used in ecological studies. There is, however, a lack of studies that evaluate the ability of the NDVI to detect fine-scale variation in grassland plant community composition and species richness. Ellenberg indicators characterize the environmental preferences of plant species – and community-mean Ellenberg values have been used to explore the environmental drivers of community assembly. 2. We used variation partitioning to test the ability of satellite-based NDVI to explain community-mean Ellenberg nutrient (mN) and moisture (mF) indices, and the richness of habitat-specialist species in dry grasslands of different ages. The grasslands represent a gradient of decreasing soil nutrient status. 3. If community composition is determined by the responses of individual species to the underlying environmental conditions and if, at the same time, community composition determines the optical characteristics of the vegetation canopy, then positive relationships between the NDVI and mN and mF are expected. Many grassland specialists are intolerant of nutrient-rich soils. If specialist richness is negatively related to soil-nutrient levels, then a negative association between the NDVI and specialist richness is expected. However, because grassland community composition is not only influenced by abiotic variables but also by other spatial and temporal drivers, we included spatial variables and grassland age in the statistical analyses. 4. The NDVI explained the majority of the variation in mF, and also contributed to a substantial proportion of the variation in mN. However, variation in specialist richness and the lowest values of mN were explained by grassland age and spatial variables – but were poorly explained by the NDVI. 5. Synthesis and applications. The NDVI showed a good ability to detect variation in plant community composition, and should provide a valuable tool for assessing fine-scale environmental variation in grasslands or for monitoring changes in grassland habitat properties. However, because the concentration of grassland specialists not only depends on environmental variables but also on the age and spatial context of the grasslands, the NDVI is unlikely to allow the identification of grasslands with high numbers of specialist species.
Data from: Long livestock farming history and human landscape shaping revealed by lake sediment DNA
The reconstruction of human-driven, Earth-shaping dynamics is important for understanding past human/environment interactions and for helping human societies that currently face global changes. However, it is often challenging to distinguish the effects of the climate from human activities on environmental changes. Here we evaluate an approach based on DNA metabarcoding used on lake sediments to provide the first high-resolution reconstruction of plant cover and livestock farming history since the Neolithic Period. By comparing these data with a previous reconstruction of erosive event frequency, we show that the most intense erosion period was caused by deforestation and overgrazing by sheep and cowherds during the Late Iron Age and Roman Period. Tracking plants and domestic mammals using lake sediment DNA (lake sedDNA) is a new, promising method for tracing past human practices, and it provides a new outlook of the effects of anthropogenic factors on landscape-scale changes.
Data from: Life-history characteristics and landscape attributes as drivers of genetic variation, gene flow and fine-scale population structure in Northern Dolly Varden (Salvelinus malma malma) in Canada
The Northern Dolly Varden (Salvelinus malma malma) displays variable life-history types and occupies freshwater habitats with varying levels of connectivity. Here, we assayed microsatellite DNA variation in Northern Dolly Varden from the western Canadian Arctic to resolve landscape and life history variables driving variation in genetic diversity and population structure. Overall, genetic variation was highest in anadromous populations and lowest in those isolated above waterfalls with stream-resident forms intermediate between the two. Anadromous and isolated populations were genetically divergent from each other while no genetic differentiation was detectable between sympatric anadromous and stream-resident forms. Population structure was stable over 25 years, hierarchically organized and conformed to an isolation-by-distance pattern, but stream-isolated forms often deviated from these patterns. Gene flow occurred primarily among Yukon North Slope populations and between sympatric anadromous and resident forms. These results were sex-dependent to some extent, but were influenced more by reproductive status and life history. Our study provides novel insights into the life history, population demographic and habitat variables that shape the distribution of genetic variation and population structure in Arctic fluvial habitats while providing a spatial context for management and conservation.
Data from: Demographic modelling reveals a history of divergence with gene flow for a glacially tied stonefly in a changing post-Pleistocene landscape
Aim: Climate warming is causing extensive loss of glaciers in mountainous regions, yet our understanding of how glacial recession influences evolutionary processes and genetic diversity is limited. Linking genetic structure with the influences shaping it can improve understanding of how species respond to environmental change. Here, we used genome-scale data and demographic modelling to resolve the evolutionary history of Lednia tumana, a rare, aquatic insect endemic to alpine streams. We also employed a range of widely used data filtering approaches to quantify how they influenced population structure results. Location: Alpine streams in the Rocky Mountains of Glacier National Park, Montana, USA. Taxon: Lednia tumana, a stonefly (Order Plecoptera) in the family Nemouridae. Methods: We generated single nucleotide polymorphism data through restriction-site associated DNA sequencing to assess contemporary patterns of genetic structure for 11 L. tumana populations. Using identified clusters, we assessed demographic history through model selection and parameter estimation in a coalescent framework. During population structure analyses, we filtered our data to assess the influence of singletons, missing data and total number of markers on results. Results: Contemporary patterns of population structure indicate that L. tumana exhibits a pattern of isolation-by-distance among populations within three genetic clusters that align with geography. Mean pairwise genetic differentiation (FST) among populations was 0.033. Coalescent-based demographic modelling supported divergence with gene flow among genetic clusters since the end of the Pleistocene (~13-17 kya), likely reflecting the south-to-north recession of ice sheets that accumulated during the Wisconsin glaciation. Main conclusions: We identified a link between glacial retreat, evolutionary history and patterns of genetic diversity for a range-restricted stonefly imperiled by climate change. This finding included a history of divergence with gene flow, an unexpected conclusion for a mountaintop species. Beyond L. tumana, this study demonstrates the complexity of assessing genetic structure for weakly differentiated species, shows the degree to which rare alleles and missing data may influence results, and highlights the usefulness of genome-scale data to extend population genetic inquiry in non-model species.
Data from: A portrait of a sucker using landscape genetics: how colonization and life history undermine the idealized dendritic metapopulation
Dendritic metapopulations have been attributed unique properties by in silico studies, including an elevated genetic diversity relative to a panmictic population of equal total size. These predictions have not been rigorously tested in nature, nor has there been full consideration of the interacting effects among contemporary landscape features, colonization history and life history traits of the target species. We tested for the effects of dendritic structure as well as the relative importance of life history, environmental barriers and historical colonization on the neutral genetic structure of a longnose sucker (Catostomus catostomus) metapopulation in the Kogaluk watershed of northern Labrador, Canada. Samples were collected from eight lakes, genotyped with 17 microsatellites, and aged using opercula. Lakes varied in differentiation, historical and contemporary connectivity, and life history traits. Isolation by distance was detected only by removing two highly genetically differentiated lakes, suggesting a lack of migration–drift equilibrium and the lingering influence of historical factors on genetic structure. Bayesian analyses supported colonization via the Kogaluk's headwaters. The historical concentration of genetic diversity in headwaters inferred by this result was supported by high historical and contemporary effective sizes of the headwater lake, T-Bone. Alternatively, reduced allelic richness in headwaters confirmed the dendritic structure's influence on gene flow, but this did not translate to an elevated metapopulation effective size. A lack of equilibrium and upstream migration may have dampened the effects of dendritic structure. We suggest that interacting historical and contemporary factors prevent the achievement of the idealized traits of a dendritic metapopulation in nature.
Marginal imprint of human land use upon fire history in a mire-dominated boreal landscape of the Veps Highland, North-West Russia
<p>Spatially explicit reconstructions of fire activity in European boreal forests are rare, limiting our understanding of factors driving vegetation dynamics in this part of the boreal domain. We have developed a spatially explicit dendrochronological reconstruction of a fire regime in a mire-dominated landscape of the Veps Nature Park (North-West Russia) over the 1580-2000 CE period.</p> <p>We dated 74 fire years using 164 fire-scarred living and dead Scots pine (Pinus sylvestris L.) trees collected on 31 sites. The historical fire cycle was 91.4 years (90% confidence intervals, CI 66.2–137.6 years) over the 1580–1720 period, decreasing to 35.9 (CI 28.1–47.6 years) between 1730 and 1770, and then increasing again to 122.7 years (CI 91.0–178.0 years) over the 1780–2000 period. The reconstructed forest fire history featured a number of patterns clearly deviating from the trends documented in previous Northern European reconstructions. The most striking feature was the absence of a period with increased fire activity during the 1600s, a pattern widely observed in Fennoscandia and in Russian Karelia. We noted, however, a higher fire activity period between 1730 and 1780, resulting from the increase in early season fires.</p> <p>Land-use history of the area did not appear to have an effect on historical fire dynamics. The current FC in the Veps Highland is close to the estimates reported for the pre-industrial colonisation period in Fennoscandia, which suggests that the area's forests currently maintain their close-to-natural fire regime.</p>
Evolutionary changes in the chromatin landscape contribute to reorganization of a developmental gene network during rapid life history evolution in sea urchins
<p>Chromatin configuration is highly dynamic during embryonic development in animals, exerting an important point of control in transcriptional regulation. Yet there exists remarkably little information about the role of evolutionary changes in chromatin configuration to the evolution of gene expression and organismal traits. Genome-wide assays of chromatin configuration, coupled with whole-genome alignments, can help address this gap in knowledge in several ways. In this study, we present a comparative analysis of regulatory element sequences and accessibility throughout embryogenesis in three sea urchin species with divergent life histories: a lecithotroph <em>Heliocidaris erythrogramma</em>, a closely related planktotroph <em>H. tuberculata</em>, and a distantly related planktotroph <em>Lytechinus variegatus</em>. We identified distinct epigenetic and mutational signatures of evolutionary modifications to the function of putative <em>cis</em>-regulatory elements in <em>H. erythrogramma</em> that have accumulated non-uniformly throughout the genome, suggesting selection, rather than drift, underlies many modifications associated with the derived life history. Specifically, regulatory elements composing the sea urchin developmental gene regulatory network are enriched for signatures of positive selection and accessibility changes which may function to alter binding affinity and access of developmental transcription factors to these sites. Furthermore, regulatory element changes often correlate with divergent expression patterns of genes involved in cell type specification, morphogenesis, and development of other derived traits, suggesting these evolutionary modifications have been consequential for phenotypic evolution in <em>H. erythrogramma</em>. Collectively, our results demonstrate that selective pressures imposed by changes in developmental life history rapidly reshape the <em>cis</em>-regulatory landscape of core developmental genes to generate novel traits and embryonic programs.</p>
FIGURE 2 in Two centuries of ornithological exploration of the Rio Doce basin, southeastern Brazil. Part I-A history of the landscape, its explorers, and their collections
FIGURE 2. Map of the study area, depicting the Rio Doce Hydrographic Basin and the Rio Barra Seca Hydrographic Basin, southeastern Brazil. Main reserves are depicted in green, rivers in blue, and main cities (above 50,000 inhabitants) in black. The red star depicts the location of the tailing dam that collapsed in Bento Rodrigues in 2015.
FIGURE 10 in Two centuries of ornithological exploration of the Rio Doce basin, southeastern Brazil. Part I-A history of the landscape, its explorers, and their collections
FIGURE 10. Number of bird records obtained in the Rio Doce Basin per decade based on the database amassed on the second part of this study. Traditional sources include museum specimens and sight records. Citizen Science sources include xeno-canto and WikiAves records. Note the logarithmic scale of the Y axis.
FIGURE 6 in Two centuries of ornithological exploration of the Rio Doce basin, southeastern Brazil. Part I-A history of the landscape, its explorers, and their collections
FIGURE 6. Natural landscapes in the Rio Doce Basin: A) campos rupestres in the Serra do Cipó National Park, along the watershed between the Rio Doce and Rio S"o Francisco; B) Tabuleiro waterfall, the third largest Brazilian waterfall, height 273 m, located in the Serra do Intendente State Park; C) campos rupestres and seasonal semi-deciduous forests in the RPPN Santuário do Caraça; D) Don Helvécio lake, the largest lake (~670 ha) of the Rio Doce State Park; E and F) pristine semi-deciduous forest in the Rio Doce State Park; G and H) campos de altitude in the Caparaó National Park; I) xeric vegetation growing atop a granitic inselberg in the municipality of Mutum; J) Macuco lake in the Sooretama Biological Reserve; K) rain forest in the Sooretama Biological Reserve; L) open restinga growing on a sandy beach ridge in the mouth of Rio Doce. Photographs by Leonardo Lopes (A, B, D–F, and I), Michelle Noronha (J, K), Felipe Leite (L), and Marcelo Vasconcelos (C, G, and H).
FIGURE 1 in Two centuries of ornithological exploration of the Rio Doce basin, southeastern Brazil. Part I-A history of the landscape, its explorers, and their collections
FIGURE 1. Satellite images depicting the county of Bento Rodrigues, in the upper Rio Doce, just before (20 July 2015) and after (24 December 2015) the rupture of the Fund"o tailing dam, which released a sludge tsunami, the worst environmental disaster in Brazilian history. Source: Google Earth™.
FIGURE 8 in Two centuries of ornithological exploration of the Rio Doce basin, southeastern Brazil. Part I-A history of the landscape, its explorers, and their collections
FIGURE 8. Land cover of the Rio Doce basin in 2018. Very rare land cover categories (<0.5% of the study area) are not depicted in the legend. Source: MapBiomas, Collection 4 (http://mapbiomas.org/).
FIGURE 9 in Two centuries of ornithological exploration of the Rio Doce basin, southeastern Brazil. Part I-A history of the landscape, its explorers, and their collections
FIGURE 9. Comparison between land cover of the Rio Doce basin in 1985 and 2018. Source: MapBiomas, Collection 4 (http:// mapbiomas.org/).
FIGURE 4 in Two centuries of ornithological exploration of the Rio Doce basin, southeastern Brazil. Part I-A history of the landscape, its explorers, and their collections
FIGURE 4. Climate classification of the Rio Doce Basin, southeastern Brazil, according to K̂ppen's Climate Classification System (Alvares et al. 2013).
FIGURE 7 in Two centuries of ornithological exploration of the Rio Doce basin, southeastern Brazil. Part I-A history of the landscape, its explorers, and their collections
FIGURE 7. Anthropic landscapes in the Rio Doce Basin: A) recently burned secondary semi-deciduous forest in process of regeneration in the municipality of Araponga; B) eroded soil bank along roadside in the municipality of Açucena; C and D) degraded pasture in Açucena; E) man-made pasture with granitic inselbergs in the municipality of Mutum; F) degraded pasture and suppressed riparian forest in Mutum; G–I) wreckage in the county of Bento Rodrigues, one year after the passage of the sludge tsunami caused by the rupture of a tailing dam; the child doll symbolizes the 19 deaths caused by the disaster; J) the now heavily silted Risoleta Neves dam, where about 20 million m3 of sediment were trapped after the rupture of the tailing dam; K) the clear waters from a tributary empties into the muddy, sediment rich, water of the Rio Doce one year after the accident; L) view of the Rio Doce from the Rio Doce State Park. The riparian forests have been almost completely extirpated from the opposite bank, giving place to eucalyptus plantations. Photographs by Leonardo Lopes (A–F, L) and Felipe Leite (G–K).
Data from: Population genetic structure of the endemic rosewoods Dalbergia cochinchinensis and D. oliveri at a regional scale reflects the Indochinese landscape and life-history traits
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Data from: Life history of the Glanville fritillary butterfly in fragmented versus continuous landscapes
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Data from: Demographic modelling reveals a history of divergence with gene flow for a glacially tied stonefly in a changing post-Pleistocene landscape
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Data from: A portrait of a sucker using landscape genetics: how colonization and life history undermine the idealized dendritic metapopulation
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