Diel pCO2 variation among coral reefs and microhabitats at Lizard Island,Great Barrier Reef

Most laboratory experiments examining the effect of ocean acidification on marine organisms use stable pH/pCO₂ treatments based on average projections for the open ocean. However, pH/pCO₂ levels vary spatially and temporally in marine environments, and this variation can affect organism responses to pH/pCO₂. On coral reefs, diel pH/pCO₂ variability at the individual reef scale has been reported in a few studies, but variation among microhabitats within a reef remains poorly understood. This study determined the pH/pCO₂ variability of three different reefs, and three contrasting coral reef microhabitats (dominated by hard coral, soft coral, or open substrate) within each reef. Three SeaFET pH loggers were deployed simultaneously at the three microhabitats within a reef over a 9-day period. This was repeated at three different reefs around the Lizard Island lagoon. The loggers recorded pH_T and temperature every 5 min. Water samples were collected from each microhabitat during four points of the tidal cycle (high, low, rising, and falling) and analysed for total alkalinity and dissolved inorganic carbon. The data show a clear diel pCO₂ cycle, increasing overnight and decreasing during the day, in association with photosynthesis and respiration cycles. Diel pCO₂ differed more between reefs than between microhabitats within reefs. Variation between reefs was most likely influenced by water flow, with the more protected (low flow) reefs experiencing a greater range in pCO₂ (Δ 250 μatm) than the exposed (high flow) reefs (Δ 116 μatm). These results add to a growing body of the literature on the diel variation of pCO₂ of shallow, nearshore environments and suggest that when projecting future pCO₂ levels, it is important to consider reef metabolism as well as physical and hydrodynamic factors.

     

Molecular variation and population structure in Elymus trachycaulus and comparison with its morphologically similar E. alaskanus

Random amplified polymorphic DNA (RAPD) markers were used to determine the levels and pattern of molecular variation in four populations of Elymus trachycaulus, and to estimate genetic similarity among different populations of E. trachycaulus from British Columbia and the Northwest Territories and one population of Elymus alaskanus from the Northwest Territories. Based on 124 RAPD bands (loci), mean percent polymorphic loci for E. trachycaulus (P_P) was 67.4% (a range 41.2% to 86.3%), and mean gene diversity (H_e) for E. trachycaulus species was 0.23 (range 0.18 to 0.27). The total genetic diversity was 0.32. Differentiation among populations was 31% (F_ST = 0.31) with most of the genetic variation found within populations (69%). This pattern of genetic variation was different from that reported for inbred species in general.The authors are very grateful to Michael Bond for excellent Laboratory assistance, to Dr. Mary Barkworth for her encouragement. This study was supported by a Natural Science and Engineering Research Council (NSERC) discovery grant and by a Saint Marys University Internal grant to G.S.     

Adaptation of sorghum: characterisation of genotypic flowering responses to temperature and photoperiod

Sorghum [Sorghum bicolor (L.) Moench] is an important cereal crop grown in a wide range of tropical and temperate environments. This study was conducted to characterise the photothermal flowering responses of sorghum genotypes and to examine relationships between photothermal characteristics and environment of origin in order to better understand the phenological basis of adaptation to environment in sorghum. Twenty-four germplasm accessions and one hybrid from 24 major sorghum-growing areas were grown in a wide range of environments varying in temperature and photoperiod in India, Kenya and Mali between 1992 and 1995. Times from sowing to flowering (f) were recorded, and the responsiveness of 1/f to temperature and photoperiod was quantified using photothermal models. Times from sowing to flowering were accurately predicted in a wide range of environments using a multiplicative rate photothermal model. Significant variation in the minimum time to flower (F_m) and photoperiod sensitivity (critical photoperiod, P_c, and photoperiod-sensitivity slope, P_s) was observed among the genotypes; in contrast there was little variation in base temperature (T_b). Adaptation of sorghum to the diverse environments in which it is grown was largely determined by photoperiod sensitivity and minimum time to flower; photoperiod sensitivity determines broad adaptation to latitude (daylength), while variation in the minimum time to flower determines specific adaptation within smaller ranges of latitude, e.g. within the humid and sub-humid tropics. Received: 16 January 1999 / Accepted: 11 March 1999     

Bayesian analysis of molecular variance in pyrosequences quantifies population genetic structure across the genome of Lycaeides butterflies

The distribution of genetic variation within and among populations is commonly used to infer their demographic and evolutionary histories. This endeavour has the potential to benefit substantially from high‐throughput next‐generation sequencing technologies through a rapid increase in the amount of data available and a corresponding increase in the precision of parameter estimation. Here we report the results of a phylogeographic study of the North American butterfly genus Lycaeides using 454 sequence data. This study serves the dual purpose of demonstrating novel molecular and analytical methods for population genetic analyses with 454 sequence data and expanding our knowledge of the phylogeographic history of Lycaeides. We obtained 341 045 sequence reads from 12 populations that we were able to assemble into 15 262 contigs (most of which were variable), representing one of the largest population genetic data sets for a non‐model organism to date. We examined patterns of genetic variation using a hierarchical Bayesian analysis of molecular variance model, which provides precise estimates of genome‐level φ_ST while appropriately modelling uncertainty in locus‐specific φ_ST. We found that approximately 36% of sequence variation was partitioned among populations, suggesting historical or current isolation among the sampled populations. Estimates of pairwise genome‐level φ_ST were largely consistent with a previous phylogeographic model for Lycaeides, suggesting fragmentation into two to three refugia during Pleistocene glacial cycles followed by post‐Pleistocene range expansion and secondary contact leading to introgressive hybridization. This study demonstrates the potential of using genome‐level data to better understand the phylogeographic history of populations.     

Low levels of genetic variation inPhenakospermum guyannense (Strelitziaceae), a widespread bat-pollinated Amazonian herb

Phenakospermum guyannense is a monotypic, arborescent, long-lived monocot that is widespread in Amazonian South America. This outcrossing species is pollinated primarily by phyllostomid bats. Given these life-history characteristics,P. guyannense is expected to exhibit high levels of genetic variation and gene flow. We used isozyme electrophoresis and randomly amplified polymorphic DNA (RAPD) to characterize genetic variation in populations ofP. guyannense from French Guiana. Both measures detected a surprisingly low level of genetic variation, with only five out of twenty (25%) allozyme loci polymorphic (P), 1.35 alleles per locus (A), and an expected heterozygosity (H_e) of 0.090 at the species level. Isozymic genetic variation was even lower within populations (P = 17.5, A = 1.24, H_e = 0.074), and was corroborated by a RAPD assay that used 26 arbitrary primers (P = 3.61, A = 1.04, H_e = 0.014). Although overall levels of variation were low, the detectable variation was distributed as would be expected for an outcrossing species with extensive gene flow (mean G_ST = 0.230). We suspect thatP. guyannense is depauperate in genetic variation because of a series of bottlenecks that affected the species over this portion of its range.     

Genetic diversity of the endangered endemic Agave victoriae-reginae (Agavaceae) in the Chihuahuan Desert

Long-lived perennials are a species-rich, ecologically important component of the North American deserts, yet we know little about their genetic structure, information important for their conservation. Agave victoriae-reginae is an endemic of the Chihuahuan Desert of northern Mexico that is endangered by collection for the ornamental trade. We examined levels and patterns of variation at ten polymorphic allozyme loci in ten populations representing the range of the species. Levels of genetic variation (mean H_e= 0.335) and differentiation (mean F_ST = 0.236) were high. Phenetic clustering suggested the existence of at least three distinct groups of populations. If this pattern of variation is representative of other long-lived desert perennials, it may explain the species richness of this group and will pose a real challenge to gene conservation efforts.     

EFFECTIVE POPULATION SIZE AND GENETIC DRIFT IN TRISTYLOUS EICHHORNIA PANICULATA (PONTEDERIACEAE)

Populations of the tristylous, annual Eichhornia paniculata are markedly differentiated with respect to frequency of mating types. This variation is associated with evolutionary changes in mating system, from predominant outcrossing to high self-fertilization. To assess the potential influence of genetic drift acting on this variation, we estimated effective population size in 10 populations from northeastern Brazil using genetic and demographic methods. Effective size (N_e) was inferred from temporal changes in allele frequency at two to eight isozyme loci and also calculated using five demographic variables: 1) the number of flowering individuals (N); 2) temporal fluctuations in N; 3) variance in flower number; 4) frequency of mating types; and 5) selfing rate. Average N_e based on isozyme data was 15.8, range 3.4–70.6, and represented a fraction (mean N_e/N = 0.106) of the census number of individuals (mean N = 762.8; range: 30.5–5,040). Temporal variation in N and variance in flower number each reduced N_e to about a half of N whereas mating type frequencies and selfing rate caused only small reductions in N_e relative to N. All estimates of N_e based on demographic variables were considerably larger than those obtained from genetic data. The two kinds of estimates were in general agreement, however, when all demographic variables were combined into a single measure. Monte Carlo simulations indicated that effective size must be fewer than about 40 for drift to overcome the frequency-dependent selection that maintains the polymorphism for mating type. Applying the average N_e/N value to 167 populations censused in northeastern Brazil indicated that 72% had effective sizes below this number. This suggests that genetic drift is likely to play a dominant role in natural populations of E. paniculata.     

Environmental variation is directly responsible for short- but not long-term variation in forest-atmosphere carbon exchange

Tower‐based eddy covariance measurements of forest‐atmosphere carbon dioxide (CO₂) exchange from many sites around the world indicate that there is considerable year‐to‐year variation in net ecosystem exchange (NEE). Here, we use a statistical modeling approach to partition the interannual variability in NEE (and its component fluxes, ecosystem respiration, R_eco, and gross photosynthesis, P_gross) into two main effects: variation in environmental drivers (air and soil temperature, solar radiation, vapor pressure deficit, and soil water content) and variation in the biotic response to this environmental forcing (as characterized by the model parameters). The model is applied to a 9‐year data set from the Howland AmeriFlux site, a spruce‐dominated forest in Maine, USA. Gap‐filled flux measurements at this site indicate that the forest has been sequestering, on average, 190 g C m⁻² yr⁻¹, with a range from 130 to 270 g C m⁻² yr⁻¹. Our fitted model predicts somewhat more uptake (mean 270 g C m⁻² yr⁻¹), but interannual variation is similar, and wavelet variance analyses indicate good agreement between tower measurements and model predictions across a wide range of timescales (hours to years). Associated with the interannual variation in NEE are clear differences among years in model parameters for both R_eco and P_gross. Analysis of model predictions suggests that, at the annual time step, about 40% of the variance in modeled NEE can be attributed to variation in environmental drivers, and 55% to variation in the biotic response to this forcing. As model predictions are aggregated at longer timescales (from individual days to months to calendar year), variation in environmental drivers becomes progressively less important, and variation in the biotic response becomes progressively more important, in determining the modeled flux. There is a strong negative correlation between modeled annual P_gross and R_eco (r=−0.93, P≤0.001); two possible explanations for this correlation are discussed. The correlation promotes homeostasis of NEE: the interannual variation in modeled NEE is substantially less than that for either P_gross or R_eco     

Characterization of gene pools of three <Emphasis Type="Italic">Pinus pumila</Emphasis> (Pall.) Regel populations at the range margins

Genetic variation of Siberian dwarf pine Pinus pumila (Pall.) Regel was characterized in three marginal populations in southwestern, southern and eastern parts of the natural species range (Baikal Area, Primorye, Kamchatka) using isozyme analysis. Analysis involving 16 isozyme loci encoding ten enzyme systems was conducted. Our results confirm that P. pumila is one of the most polymorphic species in the genus Pinus. Three marginal populations exhibited high genetic variation (P ₉₅ = 68.8%, H _o = 0.247, H _e = 0.291). Populations heterogeneity and significantly high level of divergence in coniferous (F _ST = 0.050, D _N = 0.044) reflect their genetic originality. In summary, it was shown that the level of genetic variation characteristic for P. pumila in other parts of the not only is reproduced in the populations examined but even is close to maximum there.     

Ecological genetics of range size variation in Boechera spp. (Brassicaceae)

Many taxonomic groups contain both rare and widespread species, which indicates that range size can evolve quickly. Many studies have compared molecular genetic diversity, plasticity, or phenotypic traits between rare and widespread species; however, a suite of genetic attributes that unites rare species remains elusive. Here, using two rare and two widespread Boechera (Brassicaceae) species, we conduct a simultaneous comparison of quantitative trait diversity, genetic diversity, and population structure among species with highly divergent range sizes. Consistent with previous studies, we do not find strong associations between range size and within‐population genetic diversity. In contrast, we find that both the degree of phenotypic plasticity and quantitative trait structure (Q_ST) were positively correlated with range size. We also found higher F_ST: Q_ST ratios in rare species, indicative of either a greater response to stabilizing selection or a lack of additive genetic variation. While widespread species occupy more ecological and climactic space and have diverged at both traits and markers, rare species display constrained levels of population differentiation and phenotypic plasticity. Combined, our results provide evidence for a specialization–generalization trade‐off across three orders of magnitude of range size variation in the ecological model genus, Boechera.     

Relations between stomatal closure, leaf turgor and xylem vulnerability in eight tropical dry forest trees

This study examined the linkage between xylem vulnerability, stomatal response to leaf water potential (Ψ_L), and loss of leaf turgor in eight species of seasonally dry tropical forest trees. In order to maximize the potential variation in these traits species that exhibit a range of leaf habits and phenologies were selected. It was found that in all species stomatal conductance was responsive to Ψ_L over a narrow range of water potentials, and that Ψ_L inducing 50% stomatal closure was correlated with both the Ψ_L inducing a 20% loss of xylem hydraulic conductivity and leaf water potential at turgor loss in all species. In contrast, there was no correlation between the water potential causing a 50% loss of conductivity in the stem xylem, and the water potential at stomatal closure (Ψ_SC) amongst species. It was concluded that although both leaf and xylem characters are correlated with the response of stomata to Ψ_L, there is considerable flexibility in this linkage. The range of responses is discussed in terms of the differing leaf‐loss strategies exhibited by these species.     

Family outcrossing rates and neighborhood floral density in natural populations of swamp milkweed (Asclepias incarnata): potential statistical artifacts

 To evaluate how environmental and genetic factors influence mating-system evolution, accurate estimates of outcrossing rates of individual plants (families) are required. Using isozyme markers, we observed wide variation in family outcrossing rates in three natural populations of Asclepias incarnata using three statistical methods: (1) a multilocus maximum-likelihood procedure (t _m); (2) a multilocus method-of-moments procedure (t _a); and (3) a direct comparison of progeny phenotypes against maternal phenotypes (t _d). Neighborhood floral-display size was positively correlated with t _a in one population, but showed no relationship with any of the other estimates of outcrossing for any population. Monte-Carlo simulations revealed that statistical variation associated with these estimation procedures can be large enough to explain all of the observed variation in outcrossing. We also found that significant, spurious correlations with neighborhood floral display could arise, on average, 7% of the time by chance alone. Our observations suggest that it is difficult to obtain accurate estimates of outcrossing in naturally pollinated plants using the estimation procedures currently available. Moreover, we caution that attempts to interpret observed variation in family outcrossing estimates by observing variation in ecological parameters could be misleading. Received: 28 September 1998 / Accepted: 27 October 1998     

Most stomatal closure in woody species under moderate drought can be explained by stomatal responses to leaf turgor

Reduced stomatal conductance (g_s) during soil drought in angiosperms may result from effects of leaf turgor on stomata and/or factors that do not directly depend on leaf turgor, including root‐derived abscisic acid (ABA) signals. To quantify the roles of leaf turgor‐mediated and leaf turgor‐independent mechanisms in g_s decline during drought, we measured drought responses of g_s and water relations in three woody species (almond, grapevine and olive) under a range of conditions designed to generate independent variation in leaf and root turgor, including diurnal variation in evaporative demand and changes in plant hydraulic conductance and leaf osmotic pressure. We then applied these data to a process‐based g_s model and used a novel method to partition observed declines in g_s during drought into contributions from each parameter in the model. Soil drought reduced g_s by 63–84% across species, and the model reproduced these changes well (r² = 0.91, P < 0.0001, n = 44) despite having only a single fitted parameter. Our analysis concluded that responses mediated by leaf turgor could explain over 87% of the observed decline in g_s across species, adding to a growing body of evidence that challenges the root ABA‐centric model of stomatal responses to drought.     

Is life history a barrier to dispersal? Contrasting patterns of genetic differentiation along an oceanographically complex coast

Extreme variation in early life‐history strategies is considered a moderately good predictor of genetic subdivision and hence dispersal for a range of marine species. In reality, however, a good deal of population differentiation must reflect historical effects, more subtle variation in life histories, and, particularly, the interaction of larvae with oceanographic processes. Using a combination of allozyme and microsatellite markers, we show that the large‐scale genetic structure of populations of three species (direct and planktonically developing cushion stars and a planktonic developing sea anemone that is also asexually viviparous) varies consistently, in line with the predicted capacity for dispersal within three geographic regions. We detected high levels of genetic subdivision for the direct developing cushion star (F_ST = 0.6), low levels for the planktonically developing cushion star (F_ST = 0.009), and intermediate levels for the sexual/asexual sea anmone (F_ST = 0.19). These patterns are exhibited despite the highly variable patterns of current movement and the presence of biogeographic barriers. Our results suggest that, although there is large scale genetic differentiation for two species, patterns of population connectivity are remarkably consistent within major regions and do not reflect variation in major oceanographic processes or genetic discontinuity coincident with biogeographic boundaries. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 95 , 106–116.     

Ecophysiological responses to light availability in three Blechnum species (Pteridophyta, Blechnaceae) of different ecological breadth

In Chilean evergreen temperate forest, fern species of the genus Blechnum occur in diverse microhabitats ranging from large gaps to heavily shaded understoreys. We hypothesised that differences in the ecological breadth of three co-occurring Blechnum species would be associated with differences in magnitude of ecophysiological responses to light availability. We quantified the field distribution of each species in relation to diffuse light availability (% canopy openness), and measured in situ variation in photosynthetic capacity (A), dark respiration (R _d) and specific leaf area (SLA) across the light gradient. The response of SLA of each species was also evaluated in a common garden in two light conditions (understorey and forest edge). The three Blechnum species differed significantly in the range of light environments occupied (breadth: B. chilense > B. hastatum > B. mochaenum). Despite significant interspecific differences in average A and R _d, the response of these traits to light availability did not differ among species. However, there was significant interspecific variation in both the mean value and the plasticity of SLA to light availability, the species with least ecological breadth (B. mochaenum) showing a flatter reaction norm (lower response) than its two congeners. This pattern was also found in the common garden experiment. The adjustment of leaf morphology (SLA) to light availability appears to be an important mechanism of acclimation in these Blechnum species. The narrow range of light environments occupied by B. mochaenum may be at least partly attributable to its inability to display phenotypic plasticity in SLA to changes in light availability.     

Variations in the cytoplasmic region account for the heterogeneity of the chicken MHC class I (B-F) molecules

Molecular variation among major histocompatibility complex (MHC) class I (B-F) proteins from B-homozygous chickens is apparently caused by C-terminal variation. Analysis of the total B-F protein pool revealed substantial heterogeneity with two or three molecular mass constituents, each being comprised by several isoelectric focusing variants. This heterogeneity could not be reduced by enzymatic deglycosylation. By contrast, proteolytic removal of a small (M _r 1000–4000) fragment from the chain resulted in the generation of a M _r 36 000 fragment, common to all the molecular mass variants. Unlike the parent proteins, the M _r 36 000 fragment derived from isolated variants yielded identical, simple patterns in two-dimensional gel electrophoresis and identical finger prints in peptide mapping. This, together with N-terminal amino acid sequencing, as well as comparison of hydrophobicity properties of fragments obtained by gradual proteolytic digestion, indicated that the small peptide responsible for the major B-F heterogeneity was situated in the intracellular, C-terminal part.     

Comparison of Four Mendelian Loci of the California Sea Hare (Aplysia californica) from Populations of the Coast of California and the Sea of Cortez

Aplysia californica is a species widely used in neurobiology, and specimens are collected from a wide range of places along its distribution range. A. californica is endemic to the coast of California and the Gulf of California. On the west coast, this is an unusual distribution range relative to other benthic species from that region. Four polymorphic nuclear Mendelian markers were identified (three single-copy nuclear DNA loci and one microsatellite) for an initial survey of genetic variation of wild populations. F _ST values not significantly different from 0 (overall F _ST= 0.0148) suggest there was no geographic genetic population subdivision in 177 individuals examined. Received December 3, 1999; accepted March 3, 2000.     

Genetic diversity and structure of the endemic Caesalpinia hintonii complex (Leguminosae: Caesalpinioideae) in Mexico

The Caesalpinia hintonii complex is formed by five endemic species (C. hintonii, C. laxa, C. macvaughii, C. melanadenia and C. epifanioi) occurring in central Mexico. This species complex is under incipient genetic divergence as by-product of local adaptations in reproductive and morphological traits to different habitats. We estimate the genetic variation and structure of populations of this species complex to assess the extent of genetic differentiation among populations and related species along its geographic distribution. Estimations of genetic diversity and structure were done based on ten enzymes and 18 loci. Mean number of alleles per locus ranged from 1.5 to 1.9. Polymorphic loci ranged from 42.1 to 68.4. Observed (H_o: range 0.191–0.275) and expected (H_e: range 0.205–0.317) heterozygosities in this complex were higher compared with other endemic and legume species. Neis genetic diversity estimates showed that most genetic variation was found within (H_S = 0.325) rather than among populations (D_ST = 0.085). Populations of the species C. hintonii showed a considerable genetic differentiation (F_ST = 0.207). The results of genetic diversity and structure within and among populations are in accord with the great morphological differentiation described for this species complex.     

Genetic diversity of a rare species <Emphasis Type="Italic">Aristolochia contorta</Emphasis> Bunge (Aristolochiaceae) in Primorsky Krai

The herbaceous vine, twisted birthwort Aristolochia contorta Bunge, is a rare species listed in the Red Data Book of Primorsky krai (2008). On the northern boundary of its range (south of the Russian Far East), the species is represented by small isolated populations confined to the river drainages. Using allozyme analysis, genetic variation of nine natural populations of A. contorta (247 accessions), which represented the main part of the species range in Russia, was examined. The values of genetic variation indices (P = 22.7%; A = 1.28; H _o = 0.129; H _e = 0.101) were low and comparable with the data obtained for other rare plants. The proportion of unique genotypes (G/N) and Simpson’s genotypic diversity index (D) ranged from 0.32 to 0.64 and from 0.60 to 0.98, respectively. This means that A. contorta is characterized by sexual and asexual reproduction. Moreover, the ratio between these types of reproduction varied among the populations. Complete absence of inbreeding and excess of heterozygotes (F _IS = −0.282), which was low probable in case of free mating, was observed. Evidently, clonal growth and (or) apomixis enables the species to maintain certain level of heterozygosity despite of small population sizes and non-regular gene exchange.