DNA evidence for historic population size and past ecosystem impacts of gray whales

Ecosystem restoration may require returning threatened populations of ecologically pivotal species to near their former abundances, but it is often difficult to estimate historic population size of species that have been heavily exploited. Eastern Pacific gray whales play a key ecological role in their Arctic feeding grounds and are widely thought to have returned to their prewhaling abundance. Recent mortality spikes might signal that the population has reached long-term carrying capacity, but an alternative is that this decline was due to shifting climatic conditions on Arctic feeding grounds. We used a genetic approach to estimate prewhaling abundance of gray whales and report DNA variability at 10 loci that is typical of a population of approximately 76,000-118,000 individuals, approximately three to five times more numerous than today's average census size of 22,000. Coalescent simulations indicate these estimates may include the entire Pacific metapopulation, suggesting that our average measurement of approximately 96,000 individuals was probably distributed between the eastern and currently endangered western Pacific populations. These levels of genetic variation suggest the eastern population is at most at 28-56% of its historical abundance and should be considered depleted. If used to inform management, this would halve acceptable human-caused mortality for this population from 417 to 208 per year. Potentially profound ecosystem impacts may have resulted from a decline from 96,000 gray whales to the current population. At previous levels, gray whales may have seasonally resuspended 700 million cubic meters of sediment, as much as 12 Yukon Rivers, and provided food to a million sea birds.     

Adaptation of Drosophila melanogaster populations to high mutation pressure: evolutionary adjustment of mutation rates.

Evolutionary aspects of high mutation pressure were studied in laboratory populations of Drosophila melanogaster that have irradiation histories up to 600 generations. Dose-response regressions for the x-ray induction of various types of mutation were obtained from six of these populations. The sensitivity of these irradiated populations relative to an unirradiated control population was characterized by dose reduction factors. Sensitivity decreased stepwise with the stepwise increase in irradiation levels to which the populations had been exposed every generation (0 R, 2 kR, 4 kR, 8 kR; 1 R = 0.258 mC/kg) but remained the same over hundreds of generations when the irradiation levels were constant. Resistance is controlled by single genetic factors. Additional factors evolved in subpopulations exposed to increased irradiation levels, and different factors evolved in populations that were kept separate from the beginning of their irradiation histories. Two of three factors persisted in subpopulations no longer irradiated, but one factor disappeared; this last one behaved like a transposon. Factors of relative radio-resistance are stage specific (immature oocytes) and some of them are assumed to modify or control mutation-rate genes. The resistance factors enable populations to achieve an equilibrium between the amounts of environmental mutagens and intrinsic mutation rates.     

Genetic drift and within-host metapopulation dynamics of HIV-1 infection

Most HIV replication occurs in solid lymphoid tissue, which has prominent architecture at the histological level, which separates groups of productively infected CD4(+) cells. Nevertheless, current population models of HIV assume panmixis within lymphoid tissue. We present a simple "metapopulation" model of HIV replication, where the population of infected cells is comprised of a large number of small populations, each of which is established by a few founder viruses and undergoes turnover. To test this model, we analyzed viral genetic variation of infected cell subpopulations within the spleen and demonstrated the action of founder effects as well as significant variation in the extent of genetic differentiation between subpopulations among patients. The combination of founder effects and subpopulation turnover can result in an effective population size much lower than the actual population size and may contribute to the importance of genetic drift in HIV evolution despite a large number of infected cells.     

A role for molecular genetics in biological conservation.

The recognition of recent accelerated depletion of species as a consequence of human industrial development has spawned a wide interest in identifying threats to endangered species. In addition to ecological and demographic perils, it has become clear that small populations that narrowly survive demographic contraction may undergo close inbreeding, genetic drift, and loss of overall genomic variation due to allelic loss or reduction to homozygosity. I review here the consequences of such genetic depletion revealed by applying molecular population genetic analysis to four endangered mammals: African cheetah, lion, Florida panther, and humpback whale. The accumulated genetic results, combined with physiological, ecological, and ethological data, provide a multifaceted perspective of the process of species diminution. An emerging role of population genetics, phylogenetics, and phylogeography as indicators of a population's natural history and its future prognosis provides valuable data of use in the development of conservation management plans for endangered species.     

Genetic structure of Aedes aegypti populations in Thailand using mitochondrial DNA

A hierarchical population genetic study was conducted among 19 Aedes aegypti populations in Thailand from Chiang Mai in the north to Songkhla province in the south. Single-strand conformation polymorphism analysis was used to examine variation in a 359-basepair region of the NADH dehydrogenase subunit 4 mitochondrial DNA gene (ND4). Seven haplotypes were detected in two lineages previously identified in ND4 haplotypes from North America. Gene flow estimates and highly significant variation among populations within 25 kilometers implicated genetic drift and vector control efforts as major factors in genetic structure. Mantel regression analysis demonstrated no isolation by distance. Urban areas were relatively panmictic, while suburban/rural sites exhibited more restricted gene flow. Significant genetic structure among groups of collections > 100 kilometers apart is consistent with recent (approximately 50 year) expansion of Ae. aegypti from highly populated areas accompanied by founder effects, but could also reflect the overall low genetic diversity in ND4 in Thailand.     

Genetic determinants of HDL: monogenic disorders and contributions to variation

PURPOSE OF REVIEW: This review focuses on recent progress towards the characterization of genetic variations that contribute to interindividual variation in plasma high-density lipoprotein cholesterol levels in the general population. RECENT FINDINGS: Many of the genes that harbor rare mutations leading to extreme high-density lipoprotein cholesterol levels contain common variation that influences plasma high-density lipoprotein cholesterol in several study populations. Candidate gene association studies provide evidence that some of these variations have an effect on high-density lipoprotein cholesterol, dependent on epistatic interactions or environmental context. Both rare and common variations contribute to interindividual high-density lipoprotein cholesterol variation. Recent comparisons of candidate gene sequences between individuals in the tails of the high-density lipoprotein cholesterol distributions (the upper or lower 1-5%) of several study populations indicate that as many as 20% of individuals with low high-density lipoprotein cholesterol harbor a rare mutation in an investigated gene. For example, the ABCA1 gene region harbors rare mutations and common variants that contribute to interindividual high-density lipoprotein cholesterol variation in the general population. SUMMARY: The genetic control of high-density lipoprotein cholesterol level is complex. Maximizing the utility of genetic knowledge for predicting an individual's high-density lipoprotein cholesterol level or response to intervention will require a better understanding of the action of combinations of genetic variants and environmental exposures.     

Electrocardiogram of the humpback whale (Megaptera novaeangliae), with specific reference to atrioventricular transmission and ventricular excitation.

OBJECTIVES. The objective of the study was to record the electrocardiogram (ECG) of a large whale to obtain crucial data for comparative electrophysiologic analysis. BACKGROUND. The data were needed to establish the mismatch between heart size and PR interval and QRS duration in mammals. METHODS. In the waters off the coast of Newfoundland, in two humpback whales (Megaptera novaeangliae) with an estimated weight of 30,000 kg a 1-lead ECG was recorded, enabling reliable assessment of P waves and QRS complexes. RESULTS. It was found that both the PR interval (atrioventricular [AV] transmission time) and QRS duration (ventricular excitation) are extremely short for animals of this size. These findings are difficult, if not impossible, to explain on the basis of currently accepted electrophysiologic theories. However, the narrow QRS complex may be due to a very dense His-Purkinje network in the ventricular wall of whales. Alternative mechanisms that can explain the function of the mammalian AV node need to be considered and explored. CONCLUSIONS. The results of the study may be of value for the understanding of the ECG in humans.     

Comparative studies on mammalian Hoxc8 early enhancer sequence reveal a baleen whale-specific deletion of a cis-acting element

Variations in regulatory regions of developmental control genes have been implicated in the divergence of axial morphologies. To find potentially significant changes in cis-regulatory regions, we compared nucleotide sequences and activities of mammalian Hoxc8 early enhancers. The nucleotide sequence of the early enhancer region is extremely conserved among mammalian clades, with five previously described cis-acting elements, A–E, being invariant. However, a 4-bp deletion within element C of the Hoxc8 early enhancer sequence is observed in baleen whales. When assayed in transgenic mouse embryos, a baleen whale enhancer (unlike other mammalian enhancers) directs expression of the reporter gene to more posterior regions of the neural tube but fails to direct expression to posterior mesoderm. We suggest that regulation of Hoxc8 in baleen whales differs from other mammalian species and may be associated with variation in axial morphology.     

Population Genetic Structure of Southern Flounder Inferred from Multilocus DNA Profiles

Determination of stock structure is an important component of fisheries management; incorporation of molecular genetic data is an effective method for assessing differentiation among putative populations. We examined genetic variation in Southern Flounder Paralichthys lethostigma within and between the U.S. South Atlantic and Gulf of Mexico basins to improve our understanding of the scale of population structure in this wide-ranging species. Analysis of amplified fragment length polymorphism (AFLP) fingerprints and analysis of mitochondrial DNA (mtDNA) control region sequences found clear divergence between ocean basins. Based on mtDNA sequences, no genetic differentiation was detected within the U.S. South Atlantic at spatial scales that were broad (among states: North Carolina, South Carolina, Georgia, and Florida) or fine (among estuarine regions within North Carolina). Increased genetic resolution was observed with AFLP fingerprint data, and we found significant subdivision between nearly all Southern Flounder geographic populations, suggesting the presence of finer-scale genetic population structure within the U.S. South Atlantic. However, AFLP genetic cluster analysis also revealed evidence for a high degree of mixing within the Atlantic basin; patterns of variation, which included genetic similarity between South Carolina and Gulf of Mexico samples, were not aligned closely with geography. We examined the partitioning of genetic variation among groups by using analyses of molecular variance and found no evidence that North Carolina Southern Flounder, which are managed on the state level as a unit stock, are differentiated from the remainder of U.S. South Atlantic Southern Flounder. Our findings indicate only weak structure and the potential for basinwide mixing among Atlantic Southern Flounder, suggesting that cooperation among U.S. South Atlantic states will be essential for the effective assessment of stock dynamics and future management plans.     

Disrupting evolutionary processes: the effect of habitat fragmentation on collared lizards in the Missouri Ozarks

Humans affect biodiversity at the genetic, species, community, and ecosystem levels. This impact on genetic diversity is critical, because genetic diversity is the raw material of evolutionary change, including adaptation and speciation. Two forces affecting genetic variation are genetic drift (which decreases genetic variation within but increases genetic differentiation among local populations) and gene flow (which increases variation within but decreases differentiation among local populations). Humans activities often augment drift and diminish gene flow for many species, which reduces genetic variation in local populations and prevents the spread of adaptive complexes outside their population of origin, thereby disrupting adaptive processes both locally and globally within a species. These impacts are illustrated with collared lizards (Crotaphytus collaris) in the Missouri Ozarks. Forest fire suppression has reduced habitat and disrupted gene flow in this lizard, thereby altering the balance toward drift and away from gene flow. This balance can be restored by managed landscape burns. Some have argued that, although human-induced fragmentation disrupts adaptation, it will also ultimately produce new species through founder effects. However, population genetic theory and experiments predict that most fragmentation events caused by human activities will facilitate not speciation, but local extinction. Founder events have played an important role in the macroevolution of certain groups, but only when ecological opportunities are expanding rather than contracting. The general impact of human activities on genetic diversity disrupts or diminishes the capacity for adaptation, speciation, and macroevolutionary change. This impact will ultimately diminish biodiversity at all levels.     

Genetic variation of Anopheles dirus A and D (Diptera:Culicidae) in China: inferred by mtDNA-CO I gene sequences]

OBJECTIVE: To interpret genetic variation and population structure of Anopheles dirus A and D from China by molecular marker. METHODS: Samples included An. dirus A of Hainan laboratory colony (n=13), and field specimen from Mengla (n=17) and Jiangcheng (n=17) in Yunnan Province. The specimens were identified by PCR assay before study, mtDNA-CO I region was amplified and sequenced. Genetic variation and population structure was estimated according to sequence data. RESULTS: The mtDNA-CO I gene with a length of 959 bp was analyzed. There were three haplotypes in An. dirus A and six haplotypes in An. dirus D. The above haplotypes distributed in three populations uniformly. The average number of pairwise differences within Mengla population (7.4412) was greater than that of Jiangcheng (1.2794) and Hainan (1.0513) populations, which suggested that the level of genetic divergence was the highest within Mengla population. The result of hierarchical AMOVA estimation showed a limited geneflow (Fst=0.799 9), therefore the variation level in a population (20.01%) was smaller than among the populations (79.99%). CONCLUSION: The inter-specific genetic variation between An. dirus A and D in China was small and the level of divergence among individuals was high.     

Changed gene expression for candidate ageing genes in long-lived Bicyclus anynana butterflies

Candidate genes for the regulation of lifespan have emerged from studies that use mutants and genetically manipulated model organisms. However, it is rarely addressed whether these genes contribute to lifespan variation in populations of these species that capture natural standing genetic variation. Here, we explore expression variation in three candidate ageing genes, Indy, sod2, and catalase, in Bicyclus anynana, a butterfly with well understood ecology.We used lines established from natural populations and artificially selected for increased adult starvation resistance. They show a considerable increase in adult lifespan under both starvation and optimal food conditions. We measured adult butterflies of various ages, under a range of optimal and starvation diets, from two selected populations and one unselected control population.In all lines, Indy and catalase are up-regulated in response to starvation while this is not evident for sod2. Under starvation, Indy and catalase are up-regulated in, while this is not evident for sod2. Under optimal food conditions, Indy is down-regulated at a later age, with Indy expression showing relatively high inter-individual variation. We find differences between the selected lines and the unselected line. Under starvation conditions, expression is higher for catalase in one, and for sod2 in both selected lines. Importantly, sod2 expression is also higher in the selected populations under optimal food conditions.We conclude that sod2, but not Indy, is involved in the response to artificial selection for increased starvation resistance. The role of catalase is less clear because of the differences between the two selected lines. Moreover, sod2 appears to be a candidate gene that underpins the genetic correlation between starvation resistance and longevity. Our study indicates that some, but not all, genes identified through mutant screens in other organisms may underpin standing genetic variation for ageing-related traits in stocks of Bicyclus butterflies established from natural populations. Clearly, this needs to be investigated in other organisms as well, especially in the organisms to which mutants screens were applied. This information will narrow down the list of genes that underpin variation in lifespan and ageing in extant populations of organisms, and which may serve as candidate genes in humans.     

T-cell receptor variable region gene usage in T-cell populations.

We have examined T-cell receptor alpha- and beta-chain variable (V) region gene usage in T-cell populations predicted to have different major histocompatibility complex-restriction specificities. Using a sensitive ribonuclease protection assay to measure T-cell receptor mRNA levels, we found no striking differences in the usage of three V alpha genes and three V beta genes in T-cell populations from three congeneic H-2-disparate strains of mice and between the mutually exclusive Ly2+ L3T4- and Ly2- L3T4+ T-cell subpopulations. These results suggest that major histocompatibility complex restriction cannot be explained by the differential usage of nonoverlapping V alpha or V beta gene pools. In contrast, striking but unpredictable differences were seen in V gene usage in populations of T cells selected by activation with particular alloantigens.     

Source and significance of genetic polymorphism of selected parasitic protozoa

The application of biochemical and molecular techniques in parasitological studies has provided increasing evidences of genetic polymorphism among parasite populations. This review presents possible origins of genetic variation within populations of various protozoan species. Since the mode of reproduction has an important influence on genetic polymorphism within parasite populations these considerations refer mainly to some protozoan parasites which have various life cycles, e.g. Giardia, Trypanosoma, Cryptosporidium, Toxoplasma. Also other factors associated with parasites (such as: transmission and passage history in laboratory conditions; occurrence in different hosts or geographic regions; selective pressure of drugs; competitive interactions between populations) that affect parasite genetic diversity are discussed. However, the number of examined isolates of parasites and genetic markers, assortment of methods, probes, primers and reagents used is also of significance. The significance of genetic variability in parasite populations is still the subject of much interest and controversy. A simple interpretation of such variation is impossible because of the complexity of host-parasite interactions. The knowledge of parasite diversity at the nucleic acids level has continually increased, but a corect interpretation of this phenomenon requires at least the same knowledge of genetic variability in host populations. Nevertheless, genetic variability in protozoan parasites has many important implications, e.g. for taxonomy, epidemiology, control and evolution. Genetic differences within parasite populations might also be associated with phenotypic variability, e.g. virulence, antigenicity, infectivity, drug sensitivity, host preference etc.     

Association of TLR4 gene non-missense single nucleotide polymorphisms with rheumatoid arthritis in Chinese Han population

Toll-like receptor4 (TLR4) plays an important role in the induction and regulation of the innate or adaptive immune responses. Thus, the genetic variation in TLR4 gene may influence the development of autoimmune diseases such as rheumatoid arthritis (RA). Several studies have investigated the roles of genetic polymorphisms of TLR4 gene in RA, but most of these studies were restricted to two cosegregating functional missense polymorphisms Asp299Gly and Thr399Ile. To determine whether non-missense genetic polymorphisms located in regulatory region of TLR4 are related to RA in a Chinese Han population, four single nucleotide polymorphisms (SNPs) situated on 3′ untranslating region (UTR) and 5′ UTR were genotyped in 213 RA patients and 247 unrelated ethnically matched controls using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and direct sequencing techniques. Significant genetic associations were observed with the 3′ UTR SNP rs41426344 and rs7873784. The minor allele C and homozygotic variant genotype CC of rs41426344 and minor allele C of rs7873784 were identified to be risk factors for the development of RA in Chinese Han people. Furthermore, by comparing the variation allele frequencies to other populations, prevalent genetic ethnic specificity was observed in all the four SNPs. Our study suggested that the effect of non-missense polymorphisms located in regulatory region would not be neglected in disease association analysis.     

Genetic structure of sylvatic, peridomestic and domestic populations of Triatoma dimidiata (Hemiptera: Reduviidae) from an endemic zone of Boyaca, Colombia

Randomly amplified polymorphic DNA (RAPD) technique was used to study the genetic structure of sylvatic, peridomestic and domestic populations of Triatoma dimidiata. The genetic flow among them was calculated to establish the epidemiological risk of non-domiciliated populations in the transmission of Chagas disease in an endemic area of Boyaca, Colombia. A total of 83 adult specimens were studied: 26 sylvatic, 27 peridomestic and 30 domestic insects. Wright's Fst was 0.071 and the effective migration rate (Nm) 3.3, suggestive of low genetic differentiation and a movement of at least three insects per generation. The calculated percentage of polymorphic loci was 99%, confirming a large average heterozygosity due to a permanent contact between insects of the three populations. These results imply that non-domiciliated populations of T. dimidiata represent an epidemiological risk in the transmission of Chagas disease owing to the fact that they can colonize human dwellings. Close surveillance of non-strictly domiciliated species of triatomines such as T. dimidiata should entail not only the domicile but also the peridomicile and should include control programs of animal reservoirs. Houses enhancement, educational programs, surveillance of reinfestation and of individuals at risk of infection should be priorities in the control policies in endemic regions such as Boavita, Boyaca.     

中国大陆钉螺种群遗传学研究——Ⅲ.遗传变异与地理分布的关系

本研究目的是通过检测中国大陆钉螺不同种群的等位基因频率,研究种群遗传变异与相应地理分布之关系,以确定流行区现场钉螺的种群结构。结果显示,7个多态基因位点的等位基因频率地理分布呈现3种类型:均衡、分散和非连续变向分布。3个主要多态基因位点(Est—4、Got和Mdh—2)均显示了非连续变向。样本种群间遗传距离与地理距离的回归分析表明,Logistic S曲线回归为最佳拟合曲线。结合其它数据,认为分裂亚群模型是中国大陆钉螺种群的基因结构模型。     

Drift, admixture, and selection in human evolution: a study with DNA polymorphisms.

Accuracy of evolutionary analysis of populations within a species requires the testing of a large number of genetic polymorphisms belonging to many loci. We report here a reconstruction of human differentiation based on 100 DNA polymorphisms tested in five populations from four continents. The results agree with earlier conclusions based on other classes of genetic markers but reveal that Europeans do not fit a simple model of independently evolving populations with equal evolutionary rates. Evolutionary models involving early admixture are compatible with the data. Taking one such model into account, we examined through simulation whether random genetic drift alone might explain the variation among gene frequencies across populations and genes. A measure of variation among populations was calculated for each polymorphism, and its distribution for the 100 polymorphisms was compared with that expected for a drift-only hypothesis. At least two-thirds of the polymorphisms appear to be selectively neutral, but there are significant deviations at the two ends of the observed distribution of the measure of variation: a slight excess of polymorphisms with low variation and a greater excess with high variation. This indicates that a few DNA polymorphisms are affected by natural selection, rarely heterotic, and more often disruptive, while most are selectively neutral.     

Breeding structure of the sand fly Lutzomyia longipalpis (Lutz & Neiva) in Brazil.

Eleven populations of Lutzomyia longipalpis (Lutz & Neiva), the sand fly vector of Leishmania chagasi, from different areas of Brazil were analyzed for genetic variation at 16 enzyme loci. In this region, the prevalence of visceral leishmaniasis (VL) caused by L. chagasi is spotty and reproductive isolation among populations of Lu. longipalpis has been reported. It is thought that morphologically similar cryptic species with varying vectorial capacity may be responsible for the discontinuous distribution of VL. The aim was to study the genetic structure of populations within this region and to identify demes that may represent sibling species. Genotypic frequencies within populations were in close compliance to Hardy-Weinberg expectations, suggesting there are no sympatric species among these 11 populations. Levels of genetic distance between pairs of populations were very low (< 0.03), consistent with local populations within a single sand fly species. When genotypic frequency data for all populations were pooled, 9 of the 13 polymorphic loci deviated from Hardy-Weinberg expectations, indicating some degree of genetic substructuring. Estimates of effective migration rates (N(e)m) among all populations were low, 2.73, suggesting that gene flow is restricted among populations, which is probably the reason for the observed genetic substructuring.     

Mitochondrial cytochrome b variation in populations of the visceral leishmaniasis vector Lutzomyia longipalpis across eastern Brazil

A population analysis of peridomestic, light-trapped, field specimens of the phlebotomine sand fly Lutzomyia longipalpis was targeted to six locations representing a geographic transect across eastern Brazil. Mitochondrial cytochrome b gene sequences established the pattern of genetic variation among the populations. Alignment of a 261-basepair region at the 3' end of cytochrome b identified 30 haplotypes and 21 segregating sites from 78 sand flies. Pairwise comparisons indicated statistically significant population structuring between northern and southern populations, as well as structuring among the southern populations. Prominent spatial clustering was evident for two of the populations in a minimum spanning network of the haplotypes, but sequence divergence was not sufficient to indicate cryptic species.