Phylogeny and biogeography of serolid isopods (Crustacea, Isopoda, Serolidae) and the use of ribosomal expansion segments in molecular systematics

In this study, a molecular phylogenetic hypothesis for 16 species of serolid isopods (Crustacea, Isopoda, Serolidae) from Antarctic waters, the deep sea, South America, and Australia is presented. The genes used are a 500-bp fragment of the mitochondrial LSU rRNA gene and a 700-bp fragment located in the variable region V4 of the nuclear SSU rRNA gene. The species composition and monophyly of morphologically defined genera of which several members were available are confirmed by the molecular data (Ceratoserolis, Spinoserolis, and Cuspidoserolis). The molecular data also support the redefinition of Frontoserolis s.l. and Serolella and the erection of the new genera Septemserolis and Paraserolis, as proposed by W]agele. The relationship among several genera is resolved differently in the molecular hypothesis than in the two existing morphological hypotheses, however. The molecular phylogeny may have important consequences for understanding the biogeography of the Serolidae, indicating that all Antarctic species in this study form a monophyletic group which has probably derived from species with closest extant relatives in South America. All 3 species included in this study living today in deep waters (>2000 m) of the Southern Ocean are most closely related to species living on the Antarctic shelf, so that parallel colonization of the deep sea by way of polar submergence can be reconstructed. In this study, a V4 expansion segment is reported which exceeds the longest crustacean sequences known until now by more than 270 bp. Although the V4 expansion segment has proven useful for phylogenetic purposes in this study, there is circumstantial evidence that its mechanism of evolution may depend not only on inheritance of single-site substitutions, making its routine use in phylogenetic studies potentially dangerous.     

Energy and the tempo of evolution in amphibians

Aim The evolutionary speed hypothesis (ESH) attempts to explain global patterns of species richness on the basis that rates of molecular evolution and speciation in warmer climates have led to a greater accumulation of taxa at lower latitudes. A substantial alternative hypothesis to the ESH is the tropical conservatism hypothesis (TCH). However, recent tests of the TCH, using amphibians as the model taxon, have relied on the assumption that rates of molecular evolution are stable across latitudes and elevations. Here, we test for the first time for systematic variation in rates of molecular evolution across latitude and elevation among amphibians. Location The dataset is geographically diverse with samples from all continents except Antarctica and also from many of the earth's major tropical–warm temperate archipelagos. Methods We tested for substitution rate heterogeneity across climatically varying habitats with the mitochondrial RNA genes 12S and 16S. Thus, we report here on our findings for amphibians – a taxon whose phylogenetic and trophic contexts are remote from those previously tested – using genes that have also not been examined before. The study utilized paired contrasts of sister species (188 species across 18 families, including both caudates and anurans) that are spatially separated in either latitudinal or elevational dimensions. Results We found substantially faster substitution rates for species living in warmer habitats (P= 0.001–0.002) at both lower latitudes (P < 0.02) and lower elevations (P < 0.01). Main conclusions The consistency of these results with the previous studies that used quite different organisms – and in this instance also using different genes – suggests that this is a ubiquitous pattern in nature consistent with the predictions of the ESH. Recent tests of the TCH that, in estimating diversification rates, have relied on the assumption that DNA evolution occurs at a constant rate across latitudes and elevations, require reconsideration in light of the findings presented here. Our results indicate that greater caution is required when estimating dates of divergence using DNA sequence data.     

The Dependence of Crustacean Respiration Rate on Body Mass and Habitat Temperature

The respiratorion rates of Crustacea from temperate and tropical waters of the Atlantic Ocean were measured directly at habitat temperatures of 19, 25 and 29 °C. The results were analysed together with data obtained from similar investigations in previous years (Ivleva, 1977) on Crustacea from moderately cold and polar latitudes at 10, 6 and 0 °C. Variations of the values for A and k in generalized regressions (R = AWκ) for Crustacea within the temperature limits of the physiological range were shown to have quite a clear-cut and regular character. The coefficient k varied from 0.60 to 0.79 and revealed a tendency to increase as temperatures decreased. The value of A increased with rising temperature within all intervals from 0 to 30 °C. The quantitative relationship between respiration rate and temperature was evaluated by the Arrhenius equation. Statistical processing of resultant data indicated a rather close association between log A and the habitat temperature of the Crustacea but only slight deviations from the theory of empirically found values. The accelerating effect of temperature (μ) was 13 ± 0.13 keal/mol. This value was used to calculate Q₁₀, which was more convenient for practical purposes.     

Slow algae, fast fungi: exceptionally high nucleotide substitution rate differences between lichenized fungi Omphalina and their symbiotic green algae Coccomyxa

Omphalina basidiolichens are obligate mutualistic associations of a fungus of the genus Omphalina (the exhabitant) and a unicellular green alga of the genus Coccomyxa (the inhabitant). It has been suggested that symbiotic inhabitants have a lower rate of genetic change compared to exhabitants because the latter are more exposed to abiotic environmental variation and competition from other organisms. In order to test this hypothesis we compared substitution rates in the nuclear ribosomal internal transcribed spacer region (ITS1, 5.8S, ITS2) among fungal species with rates among their respective algal symbionts. To ensure valid comparisons, only taxon pairs (12) with a common evolutionary history were used. On average, substitution rates in the ITS1 portion of Omphalina pairs were 27.5 times higher than rates in the corresponding pairs of Coccomyxa since divergence from their respective ancestor at the base of the Omphalina/Coccomyxa lineage. Substitution rates in the 5.8S and the ITS2 portions were 2.4 and 18.0 times higher, respectively. The highest rate difference (43.0) was found in the ITS1 region. These are, to our knowledge, the highest differences of substitution rates reported for symbiotic organisms. We conclude that the Omphalina model system conforms to the proposed hypothesis of lower substitution rates in the inhabitant, but that the mode of transmission of the inhabitant (vertical versus horizontal) could be a prevailing factor in the regulation of unequal rates of nucleotide substitution between co-evolving symbionts. Our phylogenetic study of Coccomyxa revealed three main lineages within this genus, corresponding to free-living Coccomyxa, individuals isolated from basidiolichens Omphalina and Coccomyxa isolated from ascolichens belonging to the Peltigerales.     

A reappraisal of the concept of metabolic cold adaptation in polar marine invertebrates

The concept of 'metabolic cold adaptation', namely that polar marine ectotherms are adapted in having an elevated basal metabolic rate, has been examined in the light of recent biochemical, physiological and ecological data for Antarctic marine organisms. It is now clear that marine invertebrates from Antarctic waters are characterized by slow growth rates, low basal metabolism and reduced annual reproductive effort, and there is thus no clear evidence of the traditional view of an elevated metabolic rate. By analogy with fish, protein synthesis rates are probably also low. This suggests that the major feature of cold adaptation is a reduction in the individual total annual energy intake in comparison with ecologically similar organisms from warm water. This allows a high standing crop of suspension feeders to develop, and low temperature is thus a significant factor in the successful widespread adoption of typical K-strategies in Antarctic marine invertebrates.     

Temperature effects on summer growth rates in the Antarctic scallop, Adamussium colbecki

Annual growth rates of Antarctic marine organisms are low compared to their relatives from warmer waters. Previous studies hypothesise that high food availability during austral spring–summer may enable Antarctic invertebrates to attain comparatively high short-term growth rates despite the low temperature. Neither a temperature-growth experiment with juvenile Adamussium colbecki (Smith 1902) nor the comparison of A. colbecki summer growth rates with an empirical scallop specific growth-to-temperature relationship could confirm this hypothesis. Hence, summer growth rates of young, immature A. colbecki are strongly affected by temperature, i.e. no uncoupling from temperature.     

Effect of elevated temperature on the physiological responses of marine <Emphasis Type="Italic">Chlorella</Emphasis> strains from different latitudes

The increased frequency of heat waves due to climate change poses a threat to all organisms. Microalgae are the basis of aquatic food webs, and high temperatures have significant impacts on their adaptation and survival rates. Algae respond to environmental changes by modulating their photosynthetic rates and biochemical composition. This study aims to examine the effect of elevated temperature on similar taxa of marine Chlorella originating from different latitudes. Strains from the Antarctic, temperate zone, and the tropics were grown at various temperatures, ranging from 4 to 38, 18 to 38, and 28 to 40 °C, respectively. A pulse-amplitude modulated (PAM) fluorometer was used to assess their photosynthetic responses. Parameters including maximum quantum efficiency (F _v/F _m), relative electron transport rate (rETR), and light harvesting efficiency (α) were determined from the rapid light curves (RLCs). In addition, the composition of fatty acids was compared to evaluate changes induced by the temperature treatments. Increasing the temperature from 35 to 38 °C for both Antarctic and temperate strains and from 38 to 40 °C for the tropical strain resulted in severe inhibition of photosynthesis and suppressed growth. Although all the strains demonstrated the ability to recover from different stress levels, the tropical strain was able to recover most rapidly while the Antarctic strain had the slowest recovery. The results underline that the thermal threshold for the analysed Chlorella strains temperature ranges between 38 and 40 °C. Furthermore, the analysed strains exhibited different trends in their response to elevated temperatures and recovery capabilities.     

Post-glacial partitioning of mitochondrial genetic variation in the field vole

Genetic markers are often used to examine population history. There is considerable debate about the behaviour of molecular clock rates around the population-species transition. Nevertheless, appropriate calibration is critical to any inference regarding the absolute timing and scale of demographic changes. Here, we use a mitochondrial cytochrome b gene genealogy, based entirely on modern sequences and calibrated from recent geophysical events, to date the post-glacial expansion of the Eurasian field vole (Microtus agrestis), a widespread temperate mammal species. The phylogeographic structure reflects the subsequent expansion of populations that went through bottlenecks at the time of the Younger Dryas (ca 12,000 years BP) rather than the Last Glacial Maximum (LGM, ca 24,000 years BP), which is usually seen as the time when present-day patterns were determined. The nucleotide substitution rate that was estimated here, ca 4 × 10(-7) substitutions/site/year, remains extremely high throughout the relevant time frame. Calibration with similarly high population-based substitution rates, rather than long-term rates derived from species divergence times, will show that post-LGM climatic events generated current phylogeographic structure in many other organisms from temperate latitudes.     

Metabolic rate is negatively linked to adult survival but does not explain latitudinal differences in songbirds

Survival rates vary dramatically among species and predictably across latitudes, but causes of this variation are unclear. The rate‐of‐living hypothesis posits that physiological damage from metabolism causes species with faster metabolic rates to exhibit lower survival rates. However, whether increased survival commonly observed in tropical and south temperate latitudes is associated with slower metabolic rate remains unclear. We compared metabolic rates and annual survival rates that we measured across 46 species, and from literature data across 147 species of birds in northern, southern and tropical latitudes. High metabolic rates were associated with lower survival but survival varied substantially among latitudinal regions independent of metabolism. The inability of metabolic rate to explain latitudinal variation in survival suggests (1) species may evolve physiological mechanisms that mitigate physiological damage from cellular metabolism and (2) extrinsic rather than intrinsic sources of mortality are the primary causes of latitudinal differences in survival.     

Ascomycota has a faster evolutionary rate and higher species diversity than Basidiomycota

Differences in rates of nucleotide or amino acid substitutions among major groups of organisms are repeatedly found and well documented. A growing body of evidence suggests a link between the rate of neutral molecular change within populations and the evolution of species diversity. More than 98% of terrestrial fungi belong to the phyla Ascomycota or Basidiomycota. The former is considerably richer in number of species than the latter. We obtained DNA sequences of 21 protein-coding genes from the lichenized fungus Rhizoplaca chrysoleuca and used them together with sequences from GenBank for subsequent analyses. Three datasets were used to test rate discrepancies between Ascomycota and Basidiomycota and that within Ascomycota: (i) 13 taxa including 105 protein-coding genes, (ii) nine taxa including 21 protein-coding genes, and (iii) nuclear LSU rDNA of 299 fungal species. Based on analyses of the 105 protein-coding genes and nuclear LSU rDNA datasets, we found that the evolutionary rate was higher in Ascomycota than in Basidiomycota. The differences in substitution rates between Ascomycota and Basidiomycota were significant. Within Ascomycota, the species-rich Sordariomycetes has the fastest evolutionary rate, while Leotiomycetes has the slowest. Our results indicate that the main contribution to the higher substitution rates in Ascomycota does not come from mutualism, ecological conditions, sterility, metabolic rate or shorter generation time, but is possibly caused by the founder effect. This is another example of the correlation between species number and evolutionary rates, which is consistent with the hypothesis that the founder effect is responsible for accelerated substitution rates in diverse clades.     

Linking fish colonization rates and water level change in littoral habitats of a Venezuelan floodplain river

Change in water level during the annual hydrologic cycle of tropical floodplain rivers results in continuous disassembly and reassembly of faunal communities in littoral habitat patches. As such, the rate of water level change should influence colonization rates of vagile organisms among habitat patches. We experimentally tested this hypothesis in a Venezuela floodplain river using artificial rocky patches as sampling units, water level change as the independent variable, and total number of individual fish that colonized a patch as the response variable. Water level significantly affected the total number of individuals that colonized patch habitats, i.e., rapidly receding waters were associated with higher colonization rates. Results suggest that water-level recession directly affects community assembly by influencing the rate at which individuals abandon and colonize local habitat patches.     

Slow algae, fast fungi: exceptionally high nucleotide substitution rate differences between lichenized fungi Omphalina and their symbiotic green algae Coccomyxa

Omphalina basidiolichens are obligate mutualistic associations of a fungus of the genus Omphalina (the exhabitant) and a unicellular green alga of the genus Coccomyxa (the inhabitant). It has been suggested that symbiotic inhabitants have a lower rate of genetic change compared to exhabitants because the latter are more exposed to abiotic environmental variation and competition from other organisms. In order to test this hypothesis we compared substitution rates in the nuclear ribosomal internal transcribed spacer region (ITS1, 5.8S, ITS2) among fungal species with rates among their respective algal symbionts. To ensure valid comparisons, only taxon pairs (12) with a common evolutionary history were used. On average, substitution rates in the ITS1 portion of Omphalina pairs were 27.5 times higher than rates in the corresponding pairs of Coccomyxa since divergence from their respective ancestor at the base of the Omphalina/Coccomyxa lineage. Substitution rates in the 5.8S and the ITS2 portions were 2.4 and 18.0 times higher, respectively. The highest rate difference (43.0) was found in the ITS1 region. These are, to our knowledge, the highest differences of substitution rates reported for symbiotic organisms. We conclude that the Omphalina model system conforms to the proposed hypothesis of lower substitution rates in the inhabitant, but that the mode of transmission of the inhabitant (vertical versus horizontal) could be a prevailing factor in the regulation of unequal rates of nucleotide substitution between co-evolving symbionts. Our phylogenetic study of Coccomyxa revealed three main lineages within this genus, corresponding to free-living Coccomyxa, individuals isolated from basidiolichens Omphalina and Coccomyxa isolated from ascolichens belonging to the Peltigerales.     

Disturbance, colonization and development of Antarctic benthic communities

A decade has yielded much progress in understanding polar disturbance and community recovery-mainly through quantifying ice scour rates, other disturbance levels, larval abundance and diversity, colonization rates and response of benthos to predicted climate change. The continental shelf around Antarctica is clearly subject to massive disturbance, but remarkably across so many scales. In summer, millions of icebergs from sizes smaller than cars to larger than countries ground out and gouge the sea floor and crush the benthic communities there, while the highest wind speeds create the highest waves to pound the coast. In winter, the calm associated with the sea surface freezing creates the clearest marine water in the world. But in winter, an ice foot encases coastal life and anchor ice rips benthos from the sea floor. Over tens and hundreds of thousands of years, glaciations have done the same on continental scales-ice sheets have bulldozed the seabed and the zoobenthos to edge of shelves. We detail and rank modern disturbance levels (from most to least): ice; asteroid impacts; sediment instability; wind/wave action; pollution; UV irradiation; volcanism; trawling; non-indigenous species; freshwater inundation; and temperature stress. Benthic organisms have had to recolonize local scourings and continental shelves repeatedly, yet a decade of studies have demonstrated that they have (compared with lower latitudes) slow tempos of reproduction, colonization and growth. Despite massive disturbance levels and slow recolonization potential, the Antarctic shelf has a much richer fauna than would be expected for its area. Now, West Antarctica is among the fastest warming regions and its organisms face new rapid changes. In the next century, temperature stress and non-indigenous species will drastically rise to become dominant disturbances to the Antarctic life. Here, we describe the potential for benthic organisms to respond to disturbance, focusing particularly on what we know now that we did not a decade ago.     

Latitudinal gradients in Atlantic reef fish communities: trophic structure and spatial use patterns

Trophic strategies and spatial use habits were investigated in reef fish communities. The results supported the hypothesis of differential use of food resources among tropical and higher latitude reef fishes, i.e . the number of species and relative abundance of fishes relying on relatively low‐quality food significantly decreased from tropical to temperate latitudes. The species : genus ratio of low‐quality food consumers increased toward the tropics, and was higher than the overall ratio considering all fishes in the assemblages. This supports the view that higher speciation rates occurred among this guild of fishes in warm waters. It was also demonstrated that density of herbivorous fishes (the dominant group relying on low‐quality food resources) in the western Atlantic decreased from tropical to temperate latitudes. Spatial use and mobility varied with latitude and consequently reef type and complexity. Fishes with small‐size home ranges predominated on tropical coral reefs.     

Could the acid–base status of Antarctic sea urchins indicate a better‐than‐expected resilience to near‐future ocean acidification?

Increasing atmospheric carbon dioxide concentration alters the chemistry of the oceans towards more acidic conditions. Polar oceans are particularly affected due to their low temperature, low carbonate content and mixing patterns, for instance upwellings. Calcifying organisms are expected to be highly impacted by the decrease in the oceans' pH and carbonate ions concentration. In particular, sea urchins, members of the phylum Echinodermata, are hypothesized to be at risk due to their high‐magnesium calcite skeleton. However, tolerance to ocean acidification in metazoans is first linked to acid–base regulation capacities of the extracellular fluids. No information on this is available to date for Antarctic echinoderms and inference from temperate and tropical studies needs support. In this study, we investigated the acid–base status of 9 species of sea urchins (3 cidaroids, 2 regular euechinoids and 4 irregular echinoids). It appears that Antarctic regular euechinoids seem equipped with similar acid–base regulation systems as tropical and temperate regular euechinoids but could rely on more passive ion transfer systems, minimizing energy requirements. Cidaroids have an acid–base status similar to that of tropical cidaroids. Therefore Antarctic cidaroids will most probably not be affected by decreasing seawater pH, the pH drop linked to ocean acidification being negligible in comparison of the naturally low pH of the coelomic fluid. Irregular echinoids might not suffer from reduced seawater pH if acidosis of the coelomic fluid pH does not occur but more data on their acid–base regulation are needed. Combining these results with the resilience of Antarctic sea urchin larvae strongly suggests that these organisms might not be the expected victims of ocean acidification. However, data on the impact of other global stressors such as temperature and of the combination of the different stressors needs to be acquired to assess the sensitivity of these organisms to global change.     

Diversity of isopods (Crustacea): new data from the Arctic and Atlantic Oceans

New data on the diversity pattern of isopods (Crustacea) from the northern most part of the North Atlantic and the Arctic Oceans is presented. The pattern of diversity with depth is similar at depths <1000m, but differs considerably below about 1000m. In the Arctic the diversity of isopods (expressed both as numbers of species per sled and expected number of species) increased with increased depth to a maximum at depths of about 320 to 1100m, but then declined towards deeper waters. There was a significant increase in numbers per sled and in the expected number of species with increased depth in the northernmost part of the North Atlantic Ocean. Additionally, changes occurred in the relative composition of the shallow and deep water fauna, with asellote isopods being relatively larger part of the isopod fauna in the Arctic than in the northern most part of the North Atlantic. This indicates major faunistic changes occurring at the Greenland-Iceland-Faeroe Ridge, possibly caused by rapid changes in the temperature. Furthermore, that the low diversity of the Arctic deep-sea is a regional phenomenon, and not a part of a large scale latitudinal pattern in the North Atlantic.     

A compound poisson process for relaxing the molecular clock

The molecular clock hypothesis remains an important conceptual and analytical tool in evolutionary biology despite the repeated observation that the clock hypothesis does not perfectly explain observed DNA sequence variation. We introduce a parametric model that relaxes the molecular clock by allowing rates to vary across lineages according to a compound Poisson process. Events of substitution rate change are placed onto a phylogenetic tree according to a Poisson process. When an event of substitution rate change occurs, the current rate of substitution is modified by a gamma-distributed random variable. Parameters of the model can be estimated using Bayesian inference. We use Markov chain Monte Carlo integration to evaluate the posterior probability distribution because the posterior probability involves high dimensional integrals and summations. Specifically, we use the Metropolis-Hastings-Green algorithm with 11 different move types to evaluate the posterior distribution. We demonstrate the method by analyzing a complete mtDNA sequence data set from 23 mammals. The model presented here has several potential advantages over other models that have been proposed to relax the clock because it is parametric and does not assume that rates change only at speciation events. This model should prove useful for estimating divergence times when substitution rates vary across lineages.     

An evaluation of the molecular clock hypothesis using mammalian DNA sequences

A statistical analysis of extensive DNA sequence data from primates, rodents, and artiodactyls clearly indicates that no global molecular clock exists in mammals. Rates of nucleotide substitution in rodents are estimated to be four to eight times higher than those in higher primates and two to four times higher than those in artiodactyls. There is strong evidence for lower substitution rates in apes and humans than in monkeys, supporting the hominoid slowdown hypothesis. There is also evidence for lower rates in humans than in apes, suggesting a further rate slowdown in the human lineage after the separation of humans from apes. By contrast, substitution rates are nearly equal in mouse and rat. These results suggest that differences in generation time or, more precisely, in the number of germline DNA replications per year are the primary cause of rate differences in mammals. Further, these differences are more in line with the neutral mutation hypothesis than if the rates are the same for short- and long-living mammals.     

Food, feeding and growth rates of peracarid macro-decomposers in a Ria Formosa salt marsh, southern Portugal

The diet, feeding rates and growth rates of three species of isopod and three species of amphipod from a Ria Formosa salt marsh in southern Portugal are compared to test the hypotheses that the relative success of amphipods as macro-decomposers in salt marshes worldwide can be a) attributed to their utilizing a distinctly different range of potentially available food resources and b) attributed to them using similar food resources but at different rates.The first hypothesis was tested using a combination of gut contents analysis, stable isotope analysis and multiple-choice food preference tests. The results of all three analyses showed that there was a very broad overlap in the resource utilization curves for these species for the most abundant potential foods available in the upper salt marsh. The first hypothesis was therefore rejected.The second hypothesis was tested with palatability experiments in which consumption rates of each of the test animals were compared for each potential food offered alone. The amphipods ate all five of the foods significantly faster, consuming from 3-73× more food per unit mass than the isopods.Analyses of their relative growth rates from when released from the marsupium until first breeding, showed that amphipods have a faster growth rate than isopods in the field which is consistent with other traits in their rapid development-high fecundity life-history strategy. We conclude that these data support the second hypothesis and that their morphological adaptations to a shredding, high ingestion-rate rapid gut turnover digestive strategy enable them to have a more efficient resource acquisition rate than the slower growing, lower fecundity and slower ingestion-rate longer gut throughput time strategy of most isopods.     

Rates of nucleotide substitution in Cornaceae (Cornales)-Pattern of variation and underlying causal factors

Identifying causes of genetic divergence is a central goal in evolutionary biology. Although rates of nucleotide substitution vary among taxa and among genes, the causes of this variation tend to be poorly understood. In the present study, we examined the rate and pattern of molecular evolution for five DNA regions over a phylogeny of Cornus, the single genus of Cornaceae. To identify evolutionary mechanisms underlying the molecular variation, we employed Bayesian methods to estimate divergence times and to infer how absolute rates of synonymous and nonsynonymous substitutions and their ratios change over time. We found that the rates vary among genes, lineages, and through time, and differences in mutation rates, selection type and intensity, and possibly genetic drift all contributed to the variation of substitution rates observed among the major lineages of Cornus. We applied independent contrast analysis to explore whether speciation rates are linked to rates of molecular evolution. The results showed no relationships for individual genes, but suggested a possible localized link between species richness and rate of nonsynonymous nucleotide substitution for the combined cpDNA regions. Furthermore, we detected a positive correlation between rates of molecular evolution and morphological change in Cornus. This was particularly pronounced in the dwarf dogwood lineage, in which genome-wide acceleration in both molecular and morphological evolution has likely occurred.