Conlan KE, Kvitek RG. 2005. Recolonization of soft-sediment ice scours on an exposed Arctic coast. Marine Ecology Progress Series 286: 21-42.
These authors monitored the occurrence, aging, and biotic recolonization of ice scours in the Barrow Strait near Resolute, Nunavut. Ice structures with deep keels, such as icebergs locked in pack ice, can scour the soft bottom even at depths approaching 100m. Scours can be 10 to 15 meters deep, hundreds of meters wide, and kilometers long, though many are smaller than that. A scour forms a characteristic geomorphology, with a deep trough that may include multiple parallel sub-troughs, bordered by berms that may be 4-5m tall relative to unscoured adjacent seabed. The benthos of Barrow Strait is hard-packed clay armored with cobble, a glacial till that lies about 5m thick above the bedrock.
Ice scours remove the cobble, and the berms are much softer than either the troughs or adjacent unscoured seabed. These authors, and a large crew of assistants, sampled the macroinvertebrates of the seabed by cores collected by SCUBA. The faunal analysis was by seiving the samples, fixing specimens in 4% Formalin and preserving them in 70% Ethanol. Most specimens were identified to family or genus, but a large sample of collected polychaetes were sent to experts in Ottawa for species-level identification. Faunal composition was compared across scours, troughs and berms, unscoured seabed, and scours of various ages, monitored over a 9-year period.
Biotically, the examined portion of the Barrow Strait constitues “urchin barrens”. Sea urchins, primarily Strongelocentrotus droebachiensis and S. pallidus, are present in high density and graze on most other epibenthic and shallow-infaunal invertebrates as well as consuming most of the available algae. The invasion by urchins may be recent, as suggested by the presence of Balanus crenatus only in areas where urchins are absent, but crushed shells of this barnacle in many areas. Other macroinvertebrates found included brittle stars, gastropods, soft corals, anenomes, sea cucumbers, etc, as well as several species of bottom dwelling fishes.
In general, the authors found a pattern of biodiversity consistent with the intermediate-disturbance hypothesis. Total species richness and biomass were both higher in areas of scours compared to unscoured areas. A patch of seabed protected from most scours behind a large berm had lower total diversity. No suite of climax species was found in any undisturbed area. One species of polychaete was found only in relatively young scours, but all other species occurred in all habitats, though relative abundances varied. This pattern suggests that ice scours and their associated habitat variation may be maintaining relatively high biodiversity in this region.
Ice scours occur with a frequency of about 1.1 events per kilometer per year, similar to some other ice-scoured habitats in other polar regions. This rate may either increase or decrease with climate warming. Warmer temperatures may increase the rate of iceberg calving, increasing the supply of deep-keel ice structures. Alternately, warmer temperatures may reduce the thickness, strength, or movements of winter pack ice and associated scouring structures.
Friday, March 14, 2008
Selker 1997
Selker EU. 1997. Epigenetic phenomena in filamentous fung: useful paradigms or repeat-induced confusion? Trends in Genetics 13: 296-301.
This author reviews point mutations, methylation, and other mechanisms of gene silencing in two common model fungi, Neurospora and Ascobolus. Repeat induced point mutation (RIP) acts in Neurospora, and causes GC to AT transitions in both copies of duplicate genes, and a low level of CpG methylation in both copies. Methylation induced meiotically (MIP) acts in Ascobolus, and causes methylation without point mutation, again in both copies of duplicate genes. Both processes detect larger sequences and tandem duplications more reliably.
Methylation reduces gene expression by interfering with transcription elongation, not transcription initiation as previously suggested.
There are two components to methylation: de novo methylation of previously unmethylated sites, and maintenance of methylation through DNA replication. Maintenance may be carried out primarily by a system that preferentially methylates hemimethylated CpG sites, as are generated during DNA replication, but other mechanisms must also occur to account for a set of observations other maintenance patterns. The mechanism of de novo methylation was apparently not understood in 1997; I do not know if that situation has changed.
The author describes the phenomenon termed “quelling”, in which transformed DNA in some fungi causes gene silencing of homologous genes; I suspect this is one of the observations that led to the discovery of RNA interference (RNAi), as the author describes further evidence that quelling is caused by some factor that diffuses from the nucleus to the cytoplasm.
The author also describes transvection, in which loci that do not occur in allelic positions on chromosomes have reduced expression. I do not know how widespread this phenomenon is, or if a mechanism has been proposed since 1997.All of these epigenetic processes are considered to function in cells as defenses against transposable elements, as they all would reduce expression (and, in the case of RIP, inheritance) of actively-transposing sequences. RIP and MIP act on very large duplications, up to the scale of chromosome rearrangements; thus they preserve chromosome structure at a range of scales.
This author reviews point mutations, methylation, and other mechanisms of gene silencing in two common model fungi, Neurospora and Ascobolus. Repeat induced point mutation (RIP) acts in Neurospora, and causes GC to AT transitions in both copies of duplicate genes, and a low level of CpG methylation in both copies. Methylation induced meiotically (MIP) acts in Ascobolus, and causes methylation without point mutation, again in both copies of duplicate genes. Both processes detect larger sequences and tandem duplications more reliably.
Methylation reduces gene expression by interfering with transcription elongation, not transcription initiation as previously suggested.
There are two components to methylation: de novo methylation of previously unmethylated sites, and maintenance of methylation through DNA replication. Maintenance may be carried out primarily by a system that preferentially methylates hemimethylated CpG sites, as are generated during DNA replication, but other mechanisms must also occur to account for a set of observations other maintenance patterns. The mechanism of de novo methylation was apparently not understood in 1997; I do not know if that situation has changed.
The author describes the phenomenon termed “quelling”, in which transformed DNA in some fungi causes gene silencing of homologous genes; I suspect this is one of the observations that led to the discovery of RNA interference (RNAi), as the author describes further evidence that quelling is caused by some factor that diffuses from the nucleus to the cytoplasm.
The author also describes transvection, in which loci that do not occur in allelic positions on chromosomes have reduced expression. I do not know how widespread this phenomenon is, or if a mechanism has been proposed since 1997.All of these epigenetic processes are considered to function in cells as defenses against transposable elements, as they all would reduce expression (and, in the case of RIP, inheritance) of actively-transposing sequences. RIP and MIP act on very large duplications, up to the scale of chromosome rearrangements; thus they preserve chromosome structure at a range of scales.
Leitch and Bennett 1997
Leitch IJ, Bennett MD. 1997. Polyploidy in angiosperms. Trends in Plant Science 2: 470-476.
These authors reviewed the occurrence and patterns of polyploidy in angiosperms. The majority of “higher plants” apparently have polyploid ancestry, some quite recently reverted to diploid. Most polyploid plants appear to be allopolyploids, derived by hybridization. Allopolyploidy presents the possibility of multiple origins of hybrid polyploid taxa, which has been identified in a few species.
The evolution of duplicated genes is discussed, with an interesting section on homology-dependent gene silencing. This is a phenomenon possibly mediated by repeat-induced changes to chromatin structure, in which some copies within a gene family are silenced or their expression altered.
These authors reviewed the occurrence and patterns of polyploidy in angiosperms. The majority of “higher plants” apparently have polyploid ancestry, some quite recently reverted to diploid. Most polyploid plants appear to be allopolyploids, derived by hybridization. Allopolyploidy presents the possibility of multiple origins of hybrid polyploid taxa, which has been identified in a few species.
The evolution of duplicated genes is discussed, with an interesting section on homology-dependent gene silencing. This is a phenomenon possibly mediated by repeat-induced changes to chromatin structure, in which some copies within a gene family are silenced or their expression altered.
Pulido and Berthold 2004
Pulido F, Berthold P. 2004. Microevolutionary response to climatic change. Advances in Ecological Research 35: 151-183.
These authors summarize and examine the available empirical evidence for adaptive responses to climate change in birds. Birds are a well studied group in this context, for a variety of reasons. Previous reviews had focused on theoretical considerations, and the likelyhood and rates of adaptive evolution in response to climate change, primarily because of a general paucity of empirical data on the subject.
A few examples of phenotypic change in bird populations have been found associated with either climate change (e.g. shift in breeding dates) or with rare extreme weather events. The authors caution that a response to selection cannot be inferred simply from a phenotypic change, as more variables must be measured and / or controlled for, particularly regarding the possibility of change driven by phenotypic plasticity. At the other extreme, some studies have suggested a change driven solely by plasticity but did not provide sufficient evidence to justify that claim.In general, short-term adaptive responses may or may not be indicative of longer-term trends, as phenotypic change can occur over multiple ecological and evolutionary time scales. Some instances of very rapid adaptation are unlikely to represent long-term trends, as they are responses to inherently limited environmental changes or to temporary conditions of population genetics.
These authors summarize and examine the available empirical evidence for adaptive responses to climate change in birds. Birds are a well studied group in this context, for a variety of reasons. Previous reviews had focused on theoretical considerations, and the likelyhood and rates of adaptive evolution in response to climate change, primarily because of a general paucity of empirical data on the subject.
A few examples of phenotypic change in bird populations have been found associated with either climate change (e.g. shift in breeding dates) or with rare extreme weather events. The authors caution that a response to selection cannot be inferred simply from a phenotypic change, as more variables must be measured and / or controlled for, particularly regarding the possibility of change driven by phenotypic plasticity. At the other extreme, some studies have suggested a change driven solely by plasticity but did not provide sufficient evidence to justify that claim.In general, short-term adaptive responses may or may not be indicative of longer-term trends, as phenotypic change can occur over multiple ecological and evolutionary time scales. Some instances of very rapid adaptation are unlikely to represent long-term trends, as they are responses to inherently limited environmental changes or to temporary conditions of population genetics.
Monday, March 10, 2008
Hijmans et al. 2005
Hijmans RJ, Cameron SE, Parra JL, Jones PG, Jarvis A. 2005. Very high resolution interpolated climate surfaces for global land areas. International Journal of Climatology 25: 1965-1978.
These authors describe the release of the WorldClim database, which includes data on several climate variables for a very large number of grid squares on land surfaces on Earth. Each grid square is 30 arc-seconds across, thus at the equator these squares are 0.816 square kilometers, and smaller (finer resolution) at higher latitudes.
Data for this database come primarily from weather stations located worldwide. Altitude was estimated from a Shuttle radar mission, for all latitudes south of 60°N, and excluding Antarctica. Each grid square’s climate was estimated by a complex interpolation algorithm that is analagous to regression: it fits a continuous surface to the points, but does not necessarily go through each point.
The authors describe some of the potential sources of error in the dataset, and urge higher quality data for future updates, for example by confirmation of precise locations for weather stations, and greater standardization in weather station record-keeping and reporting.
The database can be downloaded in a variety of formats from http://www.worldclim.org/. Most files are designed for use with GIS programs. A range of biologically meaningful data (maximum and minimum temperatures per year, seasonality) have been made available as well.
These authors describe the release of the WorldClim database, which includes data on several climate variables for a very large number of grid squares on land surfaces on Earth. Each grid square is 30 arc-seconds across, thus at the equator these squares are 0.816 square kilometers, and smaller (finer resolution) at higher latitudes.
Data for this database come primarily from weather stations located worldwide. Altitude was estimated from a Shuttle radar mission, for all latitudes south of 60°N, and excluding Antarctica. Each grid square’s climate was estimated by a complex interpolation algorithm that is analagous to regression: it fits a continuous surface to the points, but does not necessarily go through each point.
The authors describe some of the potential sources of error in the dataset, and urge higher quality data for future updates, for example by confirmation of precise locations for weather stations, and greater standardization in weather station record-keeping and reporting.
The database can be downloaded in a variety of formats from http://www.worldclim.org/. Most files are designed for use with GIS programs. A range of biologically meaningful data (maximum and minimum temperatures per year, seasonality) have been made available as well.
Foote et al. 2007
Foote M, Crampton JS, Beu AG, Marshall BA, Cooper RA, Maxwell PA, Matcham I. 2007. Rise and fall of species occupancy in Cenozoic fossil mollusks. Science 318: 1131-1134.
These authors examined a large dataset of species occurences in marine / shelf fossil molluscs in New Zealand, to infer patterns of geographic range and species occupancy. These data relate to hypotheses about extinction risk associated with the size of a species’ geographic range, and the rate of decline of species in ecological to geological time scales. Occupancy was defined here as the proportion of collections in a given interval in which a given species occurs.
The majority of species studied showed a steady increase in occupancy, followed by a long decrease and eventual extinction. Other possibilities, including rapid expansion and rapid decline (truncation) were not found very often, though some species did show such patterns. These results generally support the hypothesis that large geographic ranges are associated with longer species durations and reduced extinction risk, but do not support the hypothesis that species achieve maximal geographic range shortly after speciation. Additionally, the importance of incumbancy was not supported, under which species or higher taxa survive for long periods in the face of apparently superior competitors.
The authors suggest that different processes may control occupancy over ecological versus geological time scales. Competition and dispersal may be very important over ecological scales, but geological processes such as sea-level change and tectonic activity may be more important over longer time scales.
These authors examined a large dataset of species occurences in marine / shelf fossil molluscs in New Zealand, to infer patterns of geographic range and species occupancy. These data relate to hypotheses about extinction risk associated with the size of a species’ geographic range, and the rate of decline of species in ecological to geological time scales. Occupancy was defined here as the proportion of collections in a given interval in which a given species occurs.
The majority of species studied showed a steady increase in occupancy, followed by a long decrease and eventual extinction. Other possibilities, including rapid expansion and rapid decline (truncation) were not found very often, though some species did show such patterns. These results generally support the hypothesis that large geographic ranges are associated with longer species durations and reduced extinction risk, but do not support the hypothesis that species achieve maximal geographic range shortly after speciation. Additionally, the importance of incumbancy was not supported, under which species or higher taxa survive for long periods in the face of apparently superior competitors.
The authors suggest that different processes may control occupancy over ecological versus geological time scales. Competition and dispersal may be very important over ecological scales, but geological processes such as sea-level change and tectonic activity may be more important over longer time scales.
Monday, March 3, 2008
Arif et al. 2007
Arif S, Adams DC, Wicknick JA. 2007. Bioclimatic modelling, morphology, and behaviour reveal alternative mechanisms regulating the distributions of two parapatric salamander species. Evolutionary Ecology Research 9: 843-854.
These authors examined the factors responsible for shaping the geographic ranges of two species of salamanders in the genus Plethodon. One species is broadly distributed in eastern North America (including Guelph), the other occurs only on a group of mountain peaks in western Virginia. The primary working hypothesis was that the more restricted species is so restricted partly by competitive interactions with its congener, that is it cannot expand to lower elevations because it cannot outcompete the other, and is persists in its home range mainly via the congener’s intolerance of local abiotic conditions.
This hypothesis was tested by collecting data on diet, local distribution, head morphology, agonistic behaviour, and climate factors for both species in the region where the very localized species lives. Diet was examined by stomach contents of previously-collected specimens; no difference was found, suggesting these species are not applying pressure to each other by exploitative competition. Local distribution included measurements of parameters in 18 sites, two where both species occur (sympatry), and eight sites for each species where it occurs alone (allopatry). I suppose that taken together, at a larger spatial scale, this site distribution qualifies as parapatric. Head morphology was measured for each site, and analysed by PCA. The two species differ consistently and significantly in head shape, but the sympatric populations are not more or less divergent from each other than expected by chance, implying no character displacement for these traits. Behaviour was measured by a series of encounter trials, in which individual males from allopatric populations were allowed to interact as either “residents” or “intruders”. The highly-restricted species was found, perhaps surprisingly, to behaviourally dominate the more cosmopolitan species, suggesting any competitive exclusion that may be occurring is driven in the opposite direction to the initial prediction.
Climate data came from the WORLDCLIM data set (Hijmans et al. 2005). There was high congruence between the predicted ranges of these species through modelling and the actual observed ranges, with some exceptions – the models predicted some species occurrences where they do not occur, on the other side of obvious geographic barriers such as rivers.
The main conclusion of this paper is that the very restricted range size of one species is apparently constrained by abiotic climate factors, not by competitive exclusion or similar processes. In contrast, the absence of the more cosmopolitan species from these mountain tops is apparently driven more by interspecific interactions than by abiotic factors, a situation precisely opposite that predicted by the initial hypothesis. Additionally, these authors suggest that the differences in morphology may be indicative of local adaptation, but further refinement of those data will be required to test such hypotheses.
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