•Topographic complexity determines the climatic range and patchiness of landscapes.•Heterogeneous landscapes select for better dispersal and wider climatic niches.•Heterogeneity increases species ...pool and decreases distance to track climate niche.•Climatic heterogeneity enhances both resistance and resilience to climate change.•Topography thus drives community assembly dynamics and response to climate change.
In the face of climate change, populations have two survival options − they can remain in situ and tolerate the new climatic conditions (“stay”), or they can move to track their climatic niches (“go”). For sessile and small-stature organisms like alpine plants, staying requires broad climatic tolerances, realized niche shifts due to changing biotic interactions, acclimation through plasticity, or rapid genetic adaptation. Going, in contrast, requires good dispersal and colonization capacities. Neither the magnitude of climate change experienced locally nor the capacities required for staying/going in response to climate change are constant across landscapes, and both aspects may be strongly affected by local microclimatic variation associated with topographic complexity. We combine ideas from population and community ecology to discuss the effects of topographic complexity in the landscape on the immediate “stay” or “go” opportunities of local populations and communities, and on the selective pressures that may have shaped the stay or go capacities of the species occupying contrasting landscapes. We demonstrate, using example landscapes of different topographical complexity, how species’ thermal niches could be distributed across these landscapes, and how these, in turn, may affect many population and community ecological processes that are related to adaptation or dispersal. Focusing on treeless alpine or Arctic landscapes, where temperature is expected to be a strong determinant, our theorethical framework leads to the hypothesis that populations and communities of topographically complex (rough and patchy) landscapes should be both more resistant and more resilient to climate change than those of topographically simple (flat and homogeneous) landscapes. Our theorethical framework further points to how meta-community dynamics such as mass effects in topographically complex landscapes and extinction lags in simple landscapes, may mask and delay the long-term outcomes of these landscape differences under rapidly changing climates.
Late Pliocene and Early Pleistocene epochs 3.6 to 0.8 million years ago
had climates resembling those forecasted under future warming
. Palaeoclimatic records show strong polar amplification with ...mean annual temperatures of 11-19 °C above contemporary values
. The biological communities inhabiting the Arctic during this time remain poorly known because fossils are rare
. Here we report an ancient environmental DNA
(eDNA) record describing the rich plant and animal assemblages of the Kap København Formation in North Greenland, dated to around two million years ago. The record shows an open boreal forest ecosystem with mixed vegetation of poplar, birch and thuja trees, as well as a variety of Arctic and boreal shrubs and herbs, many of which had not previously been detected at the site from macrofossil and pollen records. The DNA record confirms the presence of hare and mitochondrial DNA from animals including mastodons, reindeer, rodents and geese, all ancestral to their present-day and late Pleistocene relatives. The presence of marine species including horseshoe crab and green algae support a warmer climate than today. The reconstructed ecosystem has no modern analogue. The survival of such ancient eDNA probably relates to its binding to mineral surfaces. Our findings open new areas of genetic research, demonstrating that it is possible to track the ecology and evolution of biological communities from two million years ago using ancient eDNA.
There is still limited consensus on the evolutionary history of species-rich temperate alpine floras due to a lack of comparable and high-quality phylogenetic data covering multiple plant lineages. ...Here we reconstructed when and how European alpine plant lineages diversified, i.e., the tempo and drivers of speciation events. We performed full-plastome phylogenomics and used multi-clade comparative models applied to six representative angiosperm lineages that have diversified in European mountains (212 sampled species, 251 ingroup species total). Diversification rates remained surprisingly steady for most clades, even during the Pleistocene, with speciation events being mostly driven by geographic divergence and bedrock shifts. Interestingly, we inferred asymmetrical historical migration rates from siliceous to calcareous bedrocks, and from higher to lower elevations, likely due to repeated shrinkage and expansion of high elevation habitats during the Pleistocene. This may have buffered climate-related extinctions, but prevented speciation along elevation gradients as often documented for tropical alpine floras.
Abstract
Environmental DNA is increasingly being used to reconstruct past and present biodiversity including from freshwater ecosystems. Macrophytes are especially good environmental indicators, thus ...their environmental DNA palaeorecord might shed light on past postglacial environments.
Here, we first review and compare studies that use metagenomics, targeted capture, and various barcoding and metabarcoding markers, in order to explore how each of these methods can be used to capture aquatic vegetation diversity and change. We then investigate the extent to which such a record can be leveraged for reconstructing local environmental conditions, using a case study based on macrophyte ecological niches.
We find that, with state‐of‐the‐art DNA barcode reference libraries, using metabarcoding to target the P6 loop region of the chloroplast
trn
L (UAA) intron is optimal to maximise taxonomic resolution and the diversity of past macrophyte communities. Shotgun sequencing also retrieves a high proportion of aquatic macrophyte diversity, but has the lowest taxonomic resolution, and targeted capture needs to be more widely applied before comparisons can be made.
From our case study, we infer past aquatic habitats from sedimentary ancient DNA records of macrophyte taxa. We reconstructed Holocene thermal range, continentality, water pH, trophic status, and light conditions in northern Fennoscandia. We show an overall stability since 9,000 years ago, even though individual lakes display different trends and variation in local climatic and physico‐chemical conditions.
Combined with the availability of near‐exhaustive barcode and traits databases, metabarcoding data can support wider ecological reconstructions that are not limited to aquatic plant taxonomic inventories but can also be used to infer past changes in water conditions and their environmental drivers. Sedimentary DNA is also a powerful tool to measure present diversity, as well as to reconstruct past lacustrine and fluvial communities of aquatic macrophytes.
Metagenomics can generate data on the diet of herbivores, without the need for primer selection and PCR enrichment steps as is necessary in metabarcoding. Metagenomic approaches to diet analysis have ...remained relatively unexplored, requiring validation of bioinformatic steps. Currently, no metagenomic herbivore diet studies have utilized both chloroplast and nuclear markers as reference sequences for plant identification, which would increase the number of reads that could be taxonomically informative. Here, we explore how in silico simulation of metagenomic data sets resembling sequences obtained from faecal samples can be used to validate taxonomic assignment. Using a known list of sequences to create simulated data sets, we derived reliable identification parameters for taxonomic assignments of sequences. We applied these parameters to characterize the diet of western capercaillies (Tetrao urogallus) located in Norway, and compared the results with metabarcoding trnL P6 loop data generated from the same samples. Both methods performed similarly in the number of plant taxa identified (metagenomics 42 taxa, metabarcoding 43 taxa), with no significant difference in species resolution (metagenomics 24%, metabarcoding 23%). We further observed that while metagenomics was strongly affected by the age of faecal samples, with fresh samples outperforming old samples, metabarcoding was not affected by sample age. On the other hand, metagenomics allowed us to simultaneously obtain the mitochondrial genome of the western capercaillies, thereby providing additional ecological information. Our study demonstrates the potential of utilizing metagenomics for diet reconstruction but also highlights key considerations as compared to metabarcoding for future utilization of this technique.
One of the most entrenched binary oppositions in archaeology and anthropology has been the agriculturalist vs hunter-gatherer-fisher dichotomy fuelling a debate that this paper tackles from the ...bottom-up by seeking to reconstruct full past diets. The Japanese prehistoric Jōmon cultures survived without fully-developed agriculture for more than 10,000 years. Here we compile a comprehensive, holistic database of archaeobotanical and archaeozoological records from the two ends of the archipelago, the northernmost prefecture of Hokkaido and the southernmost island-chain of Ryukyu. The results suggest Jōmon diets varied far more geographically than they did over time, and likely cultivated taxa were important in both regions. This provides the basis for examining how fisher-hunter-gatherer diets can fulfil nutritional requirements from varied environments and were resilient in the face of environmental change.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Biogeographers claimed for more than a century that arctic plants survived glaciations in ice‐free refugia within the limits of the North European ice sheets. Molecular studies have, however, ...provided overwhelming support for postglacial immigration into northern Europe, even from the west across the Atlantic. For the first time we can here present molecular evidence strongly favouring in situ glacial persistence of two species, the rare arctic‐alpine pioneer species Sagina caespitosa and Arenaria humifusa. Both belong to the ‘west‐arctic element’ of amphi‐Atlantic disjuncts, having their few and only European occurrences well within the limits of the last glaciation. Sequencing of non‐coding regions of chloroplast DNA revealed only limited variation. However, two very distinct and partly diverse genetic groups, one East and one West Atlantic, were detected in each species based on amplified fragment length polymorphisms (AFLPs), excluding postglacial dispersal from North America as explanation for their European occurrences. Patterns of genetic diversity and distinctiveness indicate that glacial populations existed in East Greenland and/or Svalbard (A. humifusa) and in southern Scandinavia (S. caespitosa). Despite their presumed lack of long‐distance dispersal adaptations, intermixed populations in several regions indicate postglacial contact zones. Both species are declining in Nordic countries, probably due to climate change‐induced habitat loss. Little or no current connectivity between their highly fragmented and partly distinct populations call for conservation of several populations in each geographic region.
High amounts of driftwood sail across the oceans and provide habitat for organisms tolerating the rough and saline environment. Fungi have adapted to the extremely cold and saline conditions which ...driftwood faces in the high north. For the first time, we applied high-throughput sequencing to fungi residing in driftwood to reveal their taxonomic richness, community composition, and ecology in the North Atlantic. Using pyrosequencing of ITS2 amplicons obtained from 49 marine logs, we found 807 fungal operational taxonomic units (OTUs) based on clustering at 97 % sequence similarity cut-off level. The phylum Ascomycota comprised 74 % of the OTUs and 20 % belonged to Basidiomycota. The richness of basidiomycetes decreased with prolonged submersion in the sea, supporting the general view of ascomycetes being more extremotolerant. However, more than one fourth of the fungal OTUs remained unassigned to any fungal class, emphasising the need for better DNA reference data from the marine habitat. Different fungal communities were detected in coniferous and deciduous logs. Our results highlight that driftwood hosts a considerably higher fungal diversity than currently known. The driftwood fungal community is not a terrestrial relic but a speciose assemblage of fungi adapted to the stressful marine environment and different kinds of wooden substrates found in it.
Lake settlements, particularly crannogs, pose several contradictions—visible yet inaccessible, widespread yet geographically restricted, persistent yet vulnerable. To further our understanding, we ...developed the integrated use of palaeolimnological (scanning XRF, pollen, spores, diatoms, chironomids, Cladocera, microcharcoal, biogenic silica, SEM-EDS, stable-isotopes) and biomolecular (faecal stanols, bile acids, sedaDNA) analyses of crannog cores in south-west Scotland and Ireland. Both can be effective methods sets for revealing occupation chronologies and identifying on-crannog activities and practices. Strong results from sedaDNA and lipid biomarker analyses demonstrate probable on-site animal slaughter, food storage and possible feasting, suggesting multi-period, elite site associations, and the storage and protection of valuable resources.
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