Ecological divergence in the presence of gene flow in two closely related Oryza species (Oryza rufipogon and O. nivara)

Ecological divergence plays a prominent role in the process of speciation, but how divergence occurs in the face of gene flow is still less clear, and remains controversial among evolutionists. Here we investigated the nucleotide diversity, divergence and gene flow between Oryza nivara and O. rufipogon using sequences of seven chloroplast and nuclear loci. By analysing samples from 26 wild populations across the geographic ranges of the two species, we showed that both species were highly structured and O. rufipogon maintained a higher level of species‐wide diversity than O. nivara. Notably, phylogenetic, amova and F_ST analyses were unable to detect significant nucleotide differentiation between the two species. We estimated that the two species began to diverge at c. 0.16 million years ago. Our coalescent‐based simulations strongly rejected the simple isolation model of zero migration between species, but rather provided unambiguous evidence of bidirectional gene flow between species, particularly from O. rufipogon to O. nivara. Our simulations also indicated that gene flow was recurrent during the divergence process rather than arising from secondary contact after allopatric divergence. In conjunction with different morphological and life‐history traits and habitat preference in the two species, this study supports the hypothesis that these Oryza species are better treated as ecotypes that diverged quite recently and are still under the process of divergence. Importantly, we demonstrate the ecological divergence between O. rufipogon and O. nivara in the presence of significant gene flow, implying that natural selection plays a primary role in driving the divergence of the two Oryza species.     

DRG represents a family of two closely related GTP-binding proteins

In a previous publication we identified a novel human GTP-binding protein that was related to DRG, a developmentally regulated GTP-binding protein from the central nervous system of mouse. Here we demonstrate that both the human and the mouse genome possess two closely related drg genes, termed drg1 and drg2. The two genes share 62% sequence identity at the nucleotide and 58% identity at the protein level. The corresponding proteins appear to constitute a separate family within the superfamily of the GTP-binding proteins. The DRG1 and the DRG2 mRNA are widely expressed in human and mouse tissues and show a very similar distribution pattern. The human drg1 gene is located on chromosome 22q12, the human drg2 gene on chromosome 17p12. Distantly related species including Caenorhabditis elegans, Schizosaccharomyces pombe and Saccharomyces cerevisiae also possess two drg genes. In contrast, the genomes of archaebacteria (Halobium, Methanococcus, Thermoplasma) harbor only one drg gene, while eubacteria do not seem to contain any. The high conservation of the polypeptide sequences between distantly related organisms indicates an important role for DRG1 and DRG2 in a fundamental pathway.     

Differential effects of human immunodeficiency virus type 1 Vpu on the stability of BST-2/tetherin

BST-2/CD317/tetherin is a host factor that inhibits the release of HIV-1 and other unrelated viruses. A current model proposes that BST-2 physically tethers virions to the surface of virus-producing cells. The HIV-1-encoded Vpu protein effectively antagonizes the activity of BST-2. How Vpu accomplishes this task remains unclear; however, it is known that Vpu has the ability to down-modulate BST-2 from the cell surface. Here we analyzed the effects of Vpu on BST-2 by performing a series of kinetic studies with HeLa, 293T, and CEMx174 cells. Our results indicate that the surface downregulation of BST-2 is not due to an accelerated internalization or reduced recycling of internalized BST-2 but instead is caused by interference with the resupply of newly synthesized BST-2 from within the cell. While our data confirm previous reports that the high-level expression of Vpu can cause the endoplasmic reticulum (ER)-associated degradation of BST-2, we found no evidence that Vpu targets endogenous BST-2 in the ER in the course of a viral infection. Instead, we found that Vpu acts in a post-ER compartment and increases the turnover of newly synthesized mature BST-2. Our observation that Vpu does not affect the recycling of BST-2 suggests that Vpu does not act directly at the cell surface but may interfere with the trafficking of newly synthesized BST-2 to the cell surface, resulting in the accelerated targeting of BST-2 to the lysosomal compartment for degradation.     

Determinants of tetherin antagonism in the transmembrane domain of the human immunodeficiency virus type 1 Vpu protein

Tetherin (BST2/CD317) potently restricts the particle release of human immunodeficiency virus type 1 (HIV-1) mutants defective in the accessory gene vpu. Vpu antagonizes tetherin activity and induces its cell surface downregulation and degradation in a manner dependent on the transmembrane (TM) domains of both proteins. We have carried out extensive mutagenesis of the HIV-1 NL4.3 Vpu TM domain to identify three amino acid positions, A14, W22, and, to a lesser extent, A18, that are required for tetherin antagonism. Despite the mutants localizing indistinguishably from the wild-type (wt) protein and maintaining the ability to multimerize, mutation of these positions rendered Vpu incapable of coimmunoprecipitating tetherin or mediating its cell surface downregulation. Interestingly, these amino acid positions are predicted to form one face of the Vpu transmembrane alpha helix and therefore potentially contribute to an interacting surface with the transmembrane domain of tetherin either directly or by modulating the conformation of Vpu oligomers. While the equivalent of W22 is invariant in HIV-1/SIVcpz Vpu proteins, the positions of A14 and A18 are highly conserved among Vpu alleles from HIV-1 groups M and N, but not those from group O or SIVcpz that lack human tetherin (huTetherin)-antagonizing activity, suggesting that they may have contributed to the adaption of HIV-1 to human tetherin.     

Differential responses by two closely related native fishes to restoration actions

Globally, river degradation has decimated freshwater fish populations. To help reverse this trend in a southeastern Australia river, we used multiple restoration actions, including reintroduction of instream woody habitat, riparian revegetation, removal of a weir hindering fish movement, fencing out livestock, and controlling riparian weeds. We monitored the responses of native fish at the segment scale (20 km) and reach scale (0.3 km) over 7 years to assess the effectiveness of the different restoration strategies. Two closely related species, Murray cod Maccullochella peeli and trout cod Maccullochella macquariensis, increased at the restored segment compared with the control segment. However, inherent differences between river segments and low sample size hampered assessment of the mechanisms responsible for segment‐scale changes in fish abundance. In contrast, at the reach scale, only M. peeli abundance significantly increased in reaches supplemented with wood. These differential responses by 2 closely related fish species likely reflect species‐specific responses to increased habitat availability and enhanced longitudinal connectivity when the weir improved passage around a fishway. Changes in M. peeli abundance in segments supplemented with and without wood suggest an increase in carrying capacity and not simply a redistribution of individuals within the segment, facilitated the observed expansion. Our findings confirm the need to consider individual fish species' habitat preferences carefully when designing restoration interventions. Further, species‐specific responses to restoration actions provide waterway managers with precise strategies to target fish species for recovery and the potential to predict fish outcomes based on ecological preferences.     

Niche divergence of two closely related Carbula species (Insecta: Hemiptera: Pentatomidae) despite the presence of a hybrid zone

1. The extent to which ecologically divergent selection acts to maintain species boundaries in the presence of hybridisation and gene flow is not well understood. Two parapatric taxa, Carbula humerigera (Uhler) and Carbula putoni (Jakovlev), were used to test the extent to which niche differentiation might sustain divergence of related taxa despite ongoing gene flow. 2. Mitochondrial [cytochrome c oxidase subunit I (COI), cytochrome c oxidase subunit II (COII) and cytochrome b (Cytb)] and nuclear [elongation factor 1‐alpha (EF‐1α)] markers were sequenced from 383 individuals. Clusters of morphological variations were estimated and visualised using principal component analysis (PCA). Haplotype networks were constructed using median‐joining and neighbour‐net algorithm methods. Gene flows were estimated using migrate‐n analyses. Suitable habitats for each species and their sympatric distribution were predicted with ecological niche modelling (ENM). Niche comparisons were conducted using Schoener's D and Warren's I. In addition, PCA, multivariate analysis of variance (manova ) and discriminant function analysis were used to test ecological differentiation. 3. Morphological clusters and network analysis indicated that samples were generally divided into three groups (C. humerigera, C. putoni and hybrids). Ongoing gene flow was detected among the three groups, with abundant magnitudes in the sympatric region. Niche comparison and statistical analysis showed ecological differentiation between C. humerigera and C. putoni. Two potential hybrid zones were predicted in the ENM reconstruction, located along the Yanshan‐Taihang‐Qinling and Taishan mountains. 4. These results reveal a geographically delineated hybrid zone between C. humerigera and C. putoni. These two closely related Carbula species still live in different ecological niches despite hybridisation and ongoing gene flow.     

Sex and age related changes in the locomotor activity and phototactic behaviors of two closely related species of Camponotus ants

A virgin ant queen has only one opportunity in her lifetime to realize her reproductive fitness when she leaves her nest for a mating flight. After successful mating she sheds her wings, excavates a nest and starts laying eggs to initiate her own colony. Here we report the results of our study on two related species of Camponotus ants - day active Camponotus paria and night active Camponotus compressus - aimed at investigating (i) if there exist inter-species differences in the activity and phototactic behaviors of males and queens, (ii) whether these behaviors in the queen change after mating, and (iii) whether the activity rhythm of queens changes with age. We find that while activity profiles differ between C. paria and C. compressus virgin males and queens, such differences in queens disappear after mating. Once mated, the activity rhythm of queens shows little change with age; the rhythm in virgin queens, on the other hand, changes considerably. As virgins, C. paria queens are positively phototactic, while C. compressus queens are negatively phototactic. After mating, C. paria queens become less phototactic, particularly during the subjective night, while C. compressus queens remain negatively phototactic. These results indicate that there are considerable differences in the activity and phototactic behaviors of virgin queens of the two related species of Camponotus ants. Most of these differences disappear after mating, which suggests that these behaviors may have evolved primarily for the proper execution of pre-mating events.     

Characterization of closely related lactococcal starter strains which show differing patterns of bacteriophage sensitivity

AIMS: To characterize a group of closely related Lactococcus lactis subsp. lactis casein starter strains used commercially, which differ in their sensitivity to bacteriophages isolated from the same industrial environment. METHODS AND RESULTS: Nine strains of L. lactis, six of which had been used as starter cultures for lactic casein manufacture, were shown to be closely related by pulsed-field gel electrophoresis and total DNA profiles. Nineteen phages which propagated on one or more of these starter strains were isolated from industrial casein whey samples. The phages were all small isometric-headed and could be divided into five groups on the basis of host range on the nine strains. Most of the phages did not give a PCR product with primers designed to detect the two most common lactococcal small isometric phage species (936 and P335). The hosts could be divided into six groups depending on their phage sensitivity. Plasmids encoding genes for the cell envelope associated PI-type proteinase, lactose metabolism and specificity subunits of a type I restriction/modification system were identified. CONCLUSIONS: This work demonstrates how isolates of the same starter strain may come to be regarded as separate cultures because of their different origins, and how these closely related strains may differ in some of their industrially relevant characteristics. SIGNIFICANCE AND IMPACT OF THE STUDY: This situation may be very common among lactococci used as dairy starter cultures, and implies that the dairy industry worldwide depends on a small number of different strains.     

Different behavioural responses to anthropogenic noise by two closely related passerine birds

Anthropogenic noise, now common to many landscapes, can impair acoustic communication for many species, yet some birds compensate for masking by noise by altering their songs. The phylogenetic distribution of these noise-dependent signal adjustments is uncertain, and it is not known whether closely related species respond similarly to noise. Here, we investigated the influence of noise on habitat occupancy rates and vocal frequency in two congeneric vireos with similar song features. Noise exposure did not influence occupancy rates for either species, yet song features of both changed, albeit in different ways. With increases in noise levels, plumbeous vireos (Vireo plumbeus) sang shorter songs with higher minimum frequencies. By contrast, grey vireos (Vireo vicinior) sang longer songs with higher maximum frequencies. These findings support the notion that vocal plasticity may help some species occupy noisy areas, but because there were no commonalities among the signal changes exhibited by these closely related birds, it may be difficult to predict how diverse species may modify their signals in an increasingly noisy world.     

Identification of amino acids in the human tetherin transmembrane domain responsible for HIV-1 Vpu interaction and susceptibility

Tetherin, also known as BST-2/CD317/HM1.24, is an antiviral cellular protein that inhibits the release of HIV-1 particles from infected cells. HIV-1 viral protein U (Vpu) is a specific antagonist of human tetherin that might contribute to the high virulence of HIV-1. In this study, we show that three amino acid residues (I34, L37, and L41) in the transmembrane (TM) domain of human tetherin are critical for the interaction with Vpu by using a live cell-based assay. We also found that the conservation of an additional amino acid at position 45 and two residues downstream of position 22, which are absent from monkey tetherins, are required for the antagonism by Vpu. Moreover, computer-assisted structural modeling and mutagenesis studies suggest that an alignment of these four amino acid residues (I34, L37, L41, and T45) on the same helical face in the TM domain is crucial for the Vpu-mediated antagonism of human tetherin. These results contribute to the molecular understanding of human tetherin-specific antagonism by HIV-1 Vpu.     

Serine-threonine ubiquitination mediates downregulation of BST-2/tetherin and relief of restricted virion release by HIV-1 Vpu

The HIV-1 protein Vpu counteracts the antiviral activity of the innate restriction factor BST-2/tetherin by a mechanism that partly depends on its interaction with β-TrCP, a substrate adaptor for an SCF (Skp-Cullin 1-F box) E3 ubiquitin ligase complex. This suggests that Vpu stimulates the ubiquitination of BST-2 and that this underlies the relief of restriction. Here, we show that Vpu stimulates ubiquitination of BST-2. Mutation of all potential ubiquitination sites in the cytoplasmic domain of BST-2, including lysines, cysteines, serines, and threonines, abrogates Vpu-mediated ubiquitination. However, a serine-threonine-serine sequence specifically mediates the downregulation of BST-2 from the cell surface and the optimal relief of restricted virion release. Serine-threonine ubiquitination of BST-2 is likely part of the mechanism by which Vpu counteracts innate defenses.     

Demographic mechanisms in the coexistence of two closely related perennials in a fluctuating environment

The demographic variability and life history differentiation of two closely related shrubs (Atriplex canescens and A. acanthocarpa) were investigated in the Chihuahuan Desert, and the results were interpreted in the context of theories of coexistence in fluctuating environments. Demographic information was recorded during three annual intervals and analyzed employing matrix projection models. A. canescens had lower λ (finite rate of population increase), higher longevity and generation time and slower convergence to a stable population structure than A. acanthocarpa. In favorable years for recruitment (those when, for both species, λ > 1), the λ of A. acanthocarpa was higher than that of A. canescens; in unfavorable years (when λ < 1), the reverse was true. Regardless of conditions (year), A. acanthocarpa had a type 2 survivorship curve (constant rate of mortality with age), while A. canescens had a type 3 survivorship curve (declining mortality with age). Elasticity analyses highlighted the larger influence that fecundity and growth would have in modifying the λ of A. acanthocarpa in comparison to that of A. canescens. In contrast, survival would have a larger influence on the λ of A. canescens. Atriplex acanthocarpa behaved as an opportunistic species that benefitted from sporadic favorable conditions and declined rapidly when conditions deteriorated. In contrast, A. canescens behaved as a tolerant species able to withstand years when conditions were poor, but which could not gain any advantage over A. acanthocarpa when conditions improved. By each having a relative advantage over the other on opposite ends of the contrasting climatic conditions experienced in the Chihuahuan Desert, they are able to coexist. Their contrasting life histories agreed with the theoretical predictions for the operation of the two mechanisms of species coexistence in fluctuating environments: the storage effect and the relative non-linearity of competition. Based on these results, we conclude by speculating on the nature of succession in arid communities.     

Strain-specific differences in the genetic control of two closely related mycobacteria

The host response to mycobacterial infection depends on host and pathogen genetic factors. Recent studies in human populations suggest a strain specific genetic control of tuberculosis. To test for mycobacterial-strain specific genetic control of susceptibility to infection under highly controlled experimental conditions, we performed a comparative genetic analysis using the A/J- and C57BL/6J-derived recombinant congenic (RC) mouse panel infected with the Russia and Pasteur strains of Mycobacterium bovis Bacille Calmette Guérin (BCG). Bacillary counts in the lung and spleen at weeks 1 and 6 post infection were used as a measure of susceptibility. By performing genome-wide linkage analyses of loci that impact on tissue-specific bacillary burden, we were able to show the importance of correcting for strain background effects in the RC panel. When linkage analysis was adjusted on strain background, we detected a single locus on chromosome 11 that impacted on pulmonary counts of BCG Russia but not Pasteur. The same locus also controlled the splenic counts of BCG Russia but not Pasteur. By contrast, a locus on chromosome 1 which was indistinguishable from Nramp1 impacted on splenic bacillary counts of both BCG Russia and Pasteur. Additionally, dependent upon BCG strain, tissue and time post infection, we detected 9 distinct loci associated with bacillary counts. Hence, the ensemble of genetic loci impacting on BCG infection revealed a highly dynamic picture of genetic control that reflected both the course of infection and the infecting strain. This high degree of adaptation of host genetics to strain-specific pathogenesis is expected to provide a suitable framework for the selection of specific host-mycobacteria combinations during co-evolution of mycobacteria with humans.     

A chromosomal investigation of two closely related species of Spodoptera

This paper reports the first cytogenetic study of the two closely related species of noctuid moths, Spodoptera latifascia and S. descoinsi. Chromosomes were prepared using a spreading technique on warm slides. Both gonads and larval brains, which are innovating in the Lepidoptera, were used. Out of 100 specimens observed, 35 showed mitotic metaphases, which allowed chromosomes to be counted. For both species and F1 hybrids, the diploid chromosome number was 2n = 62. The chromosomes of the two species appeared dot-shaped, more rarely rod-shaped, showing little variation in size or morphology. The preparations from larval brains also suggested the existence of two levels of ploidy (haploidy and diploidy) in some nuclei. This result will need further investigation. For the first time in the Lepidoptera, in situ hybridization with Drosophila rDNA as a probe was carried out on S. latifascia and S. descoinsi. It revealed the presence of nucleolar organizing regions located at the distal part of one chromosome pair. Though no sophisticated characterization of S. latifascia and S. descoinsi was possible, it seemed that there was no major chromosomal difference. No karyotypic element could be identified as being involved in reproductive isolation between the two species.     

Analysis of closely related genes by the use of synthetic oligonucleotide probes labeled to a high specific activity

A method for labeling synthetic oligonucleotide probes to high specific activity is described. The method utilizes two partly complementary oligonucleotides that are labeled by a fill-in reaction using the Klenow fragment of DNA polymerase I and four α³²P-nucleoside triphosphates. Such probes can, in combination with Southern blot analysis, be used for routine analysis of individual genes in multigene families.     

Different pharmacological profile of two closely related endocannabinoid ester analogs

The pharmacological and neuroprotective properties of two ester analogs of the endocannabinoids, arachidonoylethyleneglycol (AA-EG) and alpha,alpha,-dimethyl arachidonoylethyleneglycol (DMA-EG), were investigated. We examined the interaction of both compounds with cannabinoid receptors (CB1 and CB2) and their efficacy in functional assays. In competition binding assays, AA-EG and DMA-EG had low potency to displace the CB1/CB2 agonist [3H]CP-55,940 in membrane preparations expressing rodent or human receptors. Binding data correlate with low efficacy of both compounds as regards to inhibition of adenylyl cyclase activity. It was also shown that DMA-EG resists hydrolysis by rat brain membranes while AA-EG undergo complete splitting under these conditions. In the cannabinoid tetrad, AA-EG induced hypomotility, analgesia, catalepsy and decreased rectal temperature indicating cannabimimetic activity. By contrast, DMA-EG was completely inactive in the same models. DMA-EG and AA-EG potently protected rat cortical neurons in culture against oxygen deprivation at nanomolar concentrations. In glutamate-induced damage, the compounds were less active protecting neurons at micromolar concentrations. The data obtained indicate that the ester endocannabinoid template can be used for the development of new compounds with potent biological activity lacking some of the undesirable behavioral side effects.     

Assembly and comparison of two closely related Brassica napus genomes

As an increasing number of plant genome sequences become available, it is clear that gene content varies between individuals, and the challenge arises to predict the gene content of a species. However, genome comparison is often confounded by variation in assembly and annotation. Differentiating between true gene absence and variation in assembly or annotation is essential for the accurate identification of conserved and variable genes in a species. Here, we present the de novo assembly of the B. napus cultivar Tapidor and comparison with an improved assembly of the Brassica napus cultivar Darmor‐bzh. Both cultivars were annotated using the same method to allow comparison of gene content. We identified genes unique to each cultivar and differentiate these from artefacts due to variation in the assembly and annotation. We demonstrate that using a common annotation pipeline can result in different gene predictions, even for closely related cultivars, and repeat regions which collapse during assembly impact whole genome comparison. After accounting for differences in assembly and annotation, we demonstrate that the genome of Darmor‐bzh contains a greater number of genes than the genome of Tapidor. Our results are the first step towards comparison of the true differences between B. napus genomes and highlight the potential sources of error in future production of a B. napus pangenome.