Context Dependence of Local Adaptation to Abiotic and Biotic Environments: A Quantitative and Qualitative Synthesis.

Understanding how spatially variable selection shapes adaptation is an area of long-standing interest in evolutionary ecology. Recent meta-analyses have quantified the extent of local adaptation, but the relative importance of abiotic and biotic factors in driving population divergence remains poorly understood. To address this gap, we combined a quantitative meta-analysis and a qualitative metasynthesis to (1) quantify the magnitude of local adaptation to abiotic and biotic factors and (2) characterize major themes that influence the motivation and design of experiments that seek to test for local adaptation. Using local-foreign contrasts as a metric of local adaptation (or maladaptation), we found that local adaptation was greater in the presence than in the absence of a biotic interactor, especially for plants. We also found that biotic environments had stronger effects on fitness than abiotic environments when ignoring whether those environments were local versus foreign. Finally, biotic effects were stronger at low latitudes, and abiotic effects were stronger at high latitudes. Our qualitative analysis revealed that the lens through which local adaptation has been examined differs for abiotic and biotic factors. It also revealed biases in the design and implementation of experiments that make quantitative results challenging to interpret and provided directions for future research.

Drought and freezing vulnerability of the isolated hybrid aspen Populus x smithii relative to its parental species, P. tremuloides and P. grandidentata.

AIM: We assessed the vulnerability of an isolated, relictual Pleistocene hybrid aspen population of conservation interest (Populus x. smithii) and the nearest populations of its parent species (Populus grandidentata and Populus tremuloides) to springtime post-bud break freezing and growing season drought stress. Response to these stressors in the three taxa was compared in terms of avoidance and tolerance. LOCATION: North American Midwest; USA. METHODS: Unique genets from the hybrid Niobrara River population and from the two parental populations were propagated in a common garden from rhizome cuttings. We tracked their phenology before and after bud break and measured their vulnerability to freezing (stem electrolyte leakage and leaf chlorophyll fluorescence) and to drought (stem hydraulic conductance, leaf osmotic potential, stomatal pore index, and gas exchange). RESULTS: Populus grandidentata was slower to leaf out, showed lower vulnerability to stem freezing and drought-induced cavitation, but exhibited a lower capacity to tolerate drought stress through leaf resistance traits compared to P. tremuloides. Hybrids were similar to P. grandidentata in their overwintering strategy, exhibiting later bud break, and in their higher resistance to stem freezing damage, but they were more similar to P. tremuloides in their higher vulnerability to drought-induced cavitation. The hybrids shared various leaf-level gas exchange traits with both parents. All aspens showed limited loss of leaf photosynthetic function following moderate freezing. MAIN CONCLUSIONS: The Niobrara River hybrid population is vulnerable to drought due to its combination of inherited drought avoidance and tolerance traits. As climate changes, P. x smithii will likely suffer from increased drought stress, while being unaffected by frost during warmer springs. The two parental species contrast in their survival mechanisms in response to climatic stress, with P. tremuloides tending toward freezing tolerance but drought avoidance and P. grandidentata tending toward freezing avoidance and drought tolerance.

Evolutionary potential varies across populations and traits in the neotropical oak Quercus oleoides.

Heritable variation in polygenic (quantitative) traits is critical for adaptive evolution and is especially important in this era of rapid climate change. In this study, we examined the levels of quantitative genetic variation of populations of the tropical tree Quercus oleoides Cham. and Schlect. for a suite of traits related to resource use and drought resistance. We tested whether quantitative genetic variation differed across traits, populations and watering treatments. We also tested potential evolutionary factors that might have shaped such a pattern: selection by climate and genetic drift. We measured 15 functional traits on 1322 1-year-old seedlings of 84 maternal half-sib families originating from five populations growing under two watering treatments in a greenhouse. We estimated the additive genetic variance, coefficient of additive genetic variation and narrow-sense heritability for each combination of traits, populations and treatments. In addition, we genotyped a total of 119 individuals (with at least 20 individuals per population) using nuclear microsatellites to estimate genetic diversity and population genetic structure. Our results showed that gas exchange traits and growth exhibited strikingly high quantitative genetic variation compared with traits related to leaf morphology, anatomy and photochemistry. Quantitative genetic variation differed between populations even at geographical scales as small as a few kilometers. Climate was associated with quantitative genetic variation, but only weakly. Genetic structure and diversity in neutral markers did not relate to coefficient of additive genetic variation. Our study demonstrates that quantitative genetic variation is not homogeneous across traits and populations of Q. oleoides. More importantly, our findings suggest that predictions about potential responses of species to climate change need to consider population-specific evolutionary characteristics.

Natural selection and neutral evolutionary processes contribute to genetic divergence in leaf traits across a precipitation gradient in the tropical oak Quercus oleoides.

The impacts of drought are expanding worldwide as a consequence of climate change. However, there is still little knowledge of how species respond to long-term selection in seasonally dry ecosystems. In this study, we used QST -FST comparisons to investigate (i) the role of natural selection on population genetic differentiation for a set of functional traits related to drought resistance in the seasonally dry tropical oak Quercus oleoides and (ii) the influence of water availability at the site of population origin and in experimental treatments on patterns of trait divergence. We conducted a thorough phenotypic characterization of 1912 seedlings from ten populations growing in field and greenhouse common gardens under replicated watering treatments. We also genotyped 218 individuals from the same set of populations using eleven nuclear microsatellites. QST distributions for leaf lamina area, specific leaf area, leaf thickness and stomatal pore index were higher than FST distribution. Results were consistent across growth environments. Genetic differentiation among populations for these functional traits was associated with the index of moisture at the origin of the populations. Together, our results suggest that drought is an important selective agent for Q. oleoides and that differences in length and severity of the dry season have driven the evolution of genetic differences in functional traits.

Potential control of human immunodeficiency virus type 1 asp expression by alternative splicing in the upstream untranslated region.

The negative-sense asp open reading frame (ORF) positioned opposite to the human immunodeficiency virus type 1 (HIV-1) env gene encodes the 189 amino acid, membrane-associated ASP protein. Negative-sense transcription, regulated by long terminal repeat sequences, has been observed early in HIV-1 infection in vitro. All subtypes of HIV-1 were scanned to detect the negative-sense asp ORF and to identify potential regulatory sequences. A series of highly conserved upstream short open reading frames (sORFs) was identified. This potential control region from HIV-1(NL4-3), containing six sORFs, was cloned upstream of the reporter gene EGFP. Expression by transfection of HEK293 cells indicated that the introduction of this sORF region inhibits EGFP reporter expression; analysis of transcripts revealed no significant changes in levels of EGFP mRNA. Reverse transcriptase-polymerase chain reaction analysis (RT-PCR) further demonstrated that the upstream sORF region undergoes alternative splicing in vitro. The most abundant product is spliced to remove sORFs I to V, leaving only the in-frame sORF VI upstream of asp. Sequence analysis revealed the presence of typical splice donor- and acceptor-site motifs. Mutation of the highly conserved splice donor and acceptor sites modulates, but does not fully relieve, inhibition of EGFP production. The strong conservation of asp and its sORFs across all HIV-1 subtypes suggests that the asp gene product may have a role in the pathogenesis of HIV-1. Alternative splicing of the upstream sORF region provides a potential mechanism for controlling expression of the asp gene.

Urinary iodine deficiency in Gippsland pregnant women: the failure of bread fortification?

OBJECTIVE: To assess iodine status and the factors that influence iodine status among a cohort of pregnant women living in Gippsland. DESIGN, PARTICIPANTS AND SETTING: Cross-sectional study of 86 pregnant women (at ≥ 28 weeks' gestation) conducted in hospital antenatal care services and private obstetrician clinics across the Gippsland region of Victoria, Australia, from 13 January 2009 to 17 February 2010. MAIN OUTCOME MEASURES: Overall proportion of pregnant women with a urinary iodine concentration (UIC) > 150 µg/L; proportion of pregnant women with a UIC >150 µg/L after the mandatory iodine fortification of bread; use of supplements containing iodine; intake of foods known to be good sources of iodine; intake of bread. RESULTS: The percentage of pregnant women with UIC >150 µg/L (indicative of iodine sufficiency) was 28%. There was no statistically significant difference in UICs before and since iodine fortification of bread. The median UIC before fortification was 96 µg/L (interquartile range [IQR], 45-153 µg/L) and since fortification was 95.5 µg/L (IQR, 60-156 µg/L). The dietary intake of iodine-rich food (including bread) and the use of appropriate supplements was insufficient to meet the increased iodine requirements during pregnancy. CONCLUSIONS: The UICs in this cohort of pregnant women are of concern, and seem unlikely to be improved by the national iodine fortification program. Pregnant women in Gippsland urgently need effective iodine education programs and encouragement to either consume iodine-rich foods or take appropriate supplements.

Increased iodine deficiency in Victoria, Australia: analysis of neonatal thyroid-stimulating hormone data, 2001 to 2006.

OBJECTIVE: To use neonatal thyroid-stimulating hormone (TSH) concentration data to measure the iodine status of the population of the Australian state of Victoria. DESIGN, PARTICIPANTS AND SETTING: Retrospective analysis of the results of 368,552 neonatal heel-prick blood tests for TSH concentration in Victoria in the years 2001-2006. MAIN OUTCOME MEASURES: Iodine deficiency as indicated by a mean percentage of neonatal TSH concentrations > 5 mIU/L of over 3% in accordance with World Health Organization, United Nations Children's Fund and International Council for the Control of Iodine Deficiency Disorder criteria; comparison of findings for the nine Department of Human Services health regions in Victoria. RESULTS: The mean percentage of neonatal TSH concentrations > 5 mIU/L ranged from 4.07% in 2001 to 9.65% in 2006, and this increase was statistically significant (P < 0.001). The populations of all nine Victorian health regions showed increasing iodine deficiency over the study period. Metropolitan populations had higher iodine deficiency than non-metropolitan populations, and this difference was also statistically significant (P < 0.05). These results are consistent with urinary iodine excretion research in Victoria. CONCLUSIONS: The high percentage of elevated TSH concentrations among newborns is of concern and requires ongoing monitoring. Neonatal TSH assay is part of routine screening in Australia, and thus offers an effective and economical method of monitoring population iodine status.

Longitudinal analysis of human immunodeficiency virus type 1 nef/long terminal repeat sequences in a cohort of long-term survivors infected from a single source.

We studied the evolution of human immunodeficiency virus type 1 (HIV-1) in a cohort of long-term survivors infected with an attenuated strain of HIV-1 acquired from a single source. Although the cohort members experienced differing clinical courses, we demonstrate similar evolution of HIV-1 nef/long-terminal repeat (LTR) sequences, characterized by progressive sequence deletions tending toward a minimal nef/LTR structure that retains only sequence elements required for viral replication. The in vivo pathogenicity of attenuated HIV-1 is therefore dictated by viral and/or host factors other than those that impose a unidirectional selection pressure on the nef/LTR region of the HIV-1 genome.

Phagocytic efficiency of monocytes and macrophages obtained from Sydney blood bank cohort members infected with an attenuated strain of HIV-1.

Defective function of monocyte-derived macrophages contributes to HIV-1 pathogenesis. We found that phagocytosis of the opportunistic pathogens Mycobacterium avium complex and Toxoplasma gondii was impaired in monocytes obtained from individuals infected with wild-type strains of HIV-1 but generally not in monocytes collected over a 6-year period from Sydney Blood Bank Cohort (SBBC) members infected with nef/long terminal repeats (LTR) region-defective strains of HIV-1. However, longitudinal analysis of phagocytosis in 1 SBBC member, C54, showed the development of defective engulfment of opportunistic pathogens at the most recent time points, coincident with the development of further molecular deletions in the nef/LTR region. Another SBBC member, C98, underwent bronchoscopy, which provided material to examine phagocytic signaling in alveolar macrophages. In contrast to normal phagocytic efficiency of C98's monocytes (over a 6-year period), defective signaling events during FcgammaR-mediated phagocytosis by C98's alveolar macrophages were observed. High basal phosphorylation within HIV-infected macrophages correlated with colocalization of tyrosine-phosphorylated proteins with HIV-1 p24 antigen rather than around the phagocytic targets as observed in uninfected cells. Thus, although phagocytic efficiency appears to be generally unimpaired in monocytes from SBBC members, evidence of impairment in recent samples from 1 SBBC member, coincident with further genetic changes within the virus, and abnormal phagocytic signaling in alveolar macrophages from another SBBC member may herald loss of attenuation of those strains.

Selectively reduced tat mRNA heralds the decline in productive human immunodeficiency virus type 1 infection in monocyte-derived macrophages.

The transcription and splicing of human immunodeficiency virus type 1 (HIV-1) mRNA in primary blood monocyte-derived macrophages (MDM) and CD4(+) peripheral blood lymphocytes (PBL) were compared to determine whether any differences might account for the slower noncytopathic infection of cells of the macrophage lineage. The expression of regulatory mRNAs during acute infection of MDM was delayed by about 12 h compared to that of PBL. In each cell type, an increase in spliced viral mRNAs slightly preceded virus production from the culture. Following the peak of productive infection, there was a proportional decrease in the expression of all regulatory mRNAs detected in PBL. In MDM, a dramatic additional decrease specifically in the tat mRNA species heralded a reduction in virus production. This decline in tat mRNA was reflected by a concomitant decrease in Tat activity in the cells and occurred with the same kinetics irrespective of the age of the cells when infected. Addition of exogenous Tat protein elicited a burst of virus production from persistently infected MDM, suggesting that the decrease in virus production from the cultures is a consequence of the reduction in tat mRNA levels. Our results show that modulation of HIV-1 mRNAs in macrophages during long-term infection, which is dependent on the period of infection rather than cell differentiation or maturation, results in a selective reduction of Tat protein levels at the commencement of a persistent, less productive phase of infection. Determination of the mechanism of this mRNA modulation may lead to novel targets for control of replication in these important viral reservoirs.

Adaptive changes after human immunodeficiency virus type 1 transmission.

Primary HIV-1 infection (PHI) is associated with a period of viremia, the resolution of which generally coincides with the development of both humoral and cellular immune responses. In this study replication-competent quasispecies were derived from virus isolated from an individual before and after seroconversion. Virus was also isolated from the presumed donor. Phenotypic and genotypic analysis of biological clones identified transmission of an R5/M-tropic phenotype. However, the ability of clones derived from the recipient to replicate in primary macrophages and PBMCs was restricted after transmission. This apparent selection process was supported by analysis of molecular clones derived from the isolated virus. Analysis of the ratio of synonymous and nonsynonymous substitutions predicted the existence of selective pressure soon after transmission, coincident with the development of HIV-1-specific antibodies. An Env trans-complementation assay demonstrated that the infectivity of a clone derived from the recipient after seroconversion was enhanced in the presence of a selected neutralizing antibody, indicating that the developing humoral immune response may have at least in part contributed to the selective pressure identified.

Characterization of interactions between transcription factors and a regulatory region spanning nt -320 to -281 of the HIV-1 LTR in T-lymphoid and non-T-lymphoid cells.

HIV-1 gene expression is regulated by the interplay of transcription factors with multiple binding motifs present within the U3, R and U5 regions of the long terminal repeat (LTR). Here we report novel DNA binding complexes (termed 9a, 9b and 9c) between nuclear proteins from T-lymphoid and non-T-lymphoid cells and a region of the U3 LTR between nucleotides (nts) -320 to -281 in the HIV strain HXB2. Complex 9b bound a motif predicted to bind E-box or c-Myb proteins and a partially overlapping dyad symmetrical motif, and included basic helix-loop-helix proteins (E12, E47 or ITF-1) but surprisingly not c-Myb. Complex 9c, which bound to a pair of GATA sites, included GATA-3 and GATA-4 in Jurkat and MT-2 cells, respectively. We also demonstrate that the c-Myb/E-box and GATA sites form a bipartite motif required for the formation of complex 9a. Transient transfection experiments with T cells revealed that in the context of a minichromosome assembled full-length LTR, mutation of region -320 to -281 increased basal and PMA-stimulated LTR activity. These findings suggest that this region is an important component of the HIV-1 LTR required for response to different cellular transcription factors.