Differences In Biological Traits Research Articles

Wind-dispersed seeds blur phylogeographic breaks: The complex evolutionary history of Populus lasiocarpa around the Sichuan Basin

The strength of phylogeographic breaks can vary among species in the same area despite being subject to the same geological and climate history due to differences in biological traits. Several important phylogeographic breaks exist around the Sichuan Basin in Southwest China but few studies have focused on wind-dispersed plants. Here, we investigated the phylogeographic patterns and the evolutionary history of Populus lasiocarpa, a wind-pollinated and wind-dispersed tree species with a circum-Sichuan Basin distribution in southwest China. We sequenced and analyzed three plastid DNA fragments (ptDNA) and eight nuclear microsatellites (nSSRs) of 265 individuals of P. lasiocarpa from 21 populations spanning the entire distribution range. Distribution patterns based on nSSR data revealed that there are three genetic groups in P. lasiocarpa. This is consistent with the three phylogeographic breaks (Sichuan Basin, the Kaiyong Line and the 105°E line), where the Sichuan basin acts as the main barrier to gene flow between western and eastern groups. However, the distribution pattern based on ptDNA haplotypes poorly matched the phylogeographic breaks, and wind-dispersed seeds may be one of the main contributing factors. Species distribution modelling suggested a larger potential distribution in the last glacial maximum with a severe bottleneck during the last interglacial. A DIYABC model also suggested a population contraction and expansion for both western and eastern lineages. These results indicate that biological traits are likely to affect the evolutionary history of plants, and that nuclear molecular markers, which experience higher levels of gene flow, might be better indicators of phylogeographic breaks.

International Consortium to Advance Cross-Species Extrapolation of the Effects of Chemicals in Regulatory Toxicology.

International Consortium to Advance Cross-Species Extrapolation of the Effects of Chemicals in Regulatory Toxicology.

Can no-bubble methane seeps affect biological traits of benthic macroinvertebrates in coastal systems?

Methane seep studies often target sites where methane gas is actively bubbling from the sea floor to the water column. However, gas bubbles often remain trapped in surficial seabed sediments, especially in coastal systems; notably few ecological studies exist for these systems. These environments form patches on the seafloor in the Bahia Blanca estuary that, based on taxonomic analysis, represent a distinct benthic habitat. Here we examine whether taxonomic changes in benthic communities associated with trapped methane gas bubbles are related to functional changes. We found significant differences in biological traits of macroinvertebrates weighted by abundance and by species between two sites differing in gas presence and between spring and winter seasons. Compared with the control (no gas) site, the gas site had subsurface-deposit feeders and large sessile animals partially calcified with suspension-feeding mode. In contrast, at the control site the small and non-calcified animals are discretely motile, building burrows and tubes and feeding on surface deposit material. Trapped methane gas, detected with seismic methods, changes biological traits in benthic fauna and can lead to alteration of some ecosystem functions. This suggests the utility of high-resolution seismic methods for detect these benthic habitats with high spatial accuracy, and a need to further understanding of ecosystem processes associated with gas presence in the context of both direct anthropogenic and climate-change pressures.

No hybridization and marked interspecific differences in individual growth rate in mixed cultures of Manila clam (Ruditapes philippinarum) and grooved carpet-shell clam (R. decussatus)

The Manila clam (Ruditapes philippinarum) was introduced in Europe in the 1970's and in the following years it became naturalized. Interactions with the native species include hybridization with the grooved carpet-shell (GCS) clam (R. decussatus), which may have both useful and undesirable consequences. Here we report an attempt to produce hybrids in captivity by crossing 3 females and 4–5 males of each species in a two-step protocol that favored hybrid fertilizations. One-hundred animals were sampled at 15 months after fertilization, and scored for one morphological diagnostic trait (siphon fusion) and two diagnostic genetic DNA markers (ITS-2 and Fas-i1). No hybrids were detected, although the 0% hybridization rate has an associated 95% confidence interval of 3.3%. This result suggests that successful hybrid fertilization may be infrequent and/or the hybrid offspring may have very low survival rate. Abundant offspring of the two parental species were obtained and provided an unprecedented opportunity to study the innate differences in biological traits between the two species without the confounding influence of environmental variability. Individuals with ripe gonads were significantly less frequent in the Manila clam, suggesting an innate trend to earlier summer spawning in this species. Manila clam grew 20% faster than GCS clam and showed 80% heavier shells. However GCS clam showed almost twice as much variability in size as Manila clam, and some individuals of this species were as large as the largest Manila clams. The observed difference in growth variability may reflect a general loss of genetic variability in Manila clam during the introduction in Europe, although a random effect from using a small number of parents in the mixed cross cannot be discarded. Discrimination between these explanations, as well as determining more precisely the occurrence of hybridization in hatcheries by studying larger numbers of parents and offspring, may help improving clam aquaculture in Europe while preserving the genetic resources of the GCS clam.

Gene Expression Profiling of Neospora caninum in Bovine Macrophages Reveals Differences Between Isolates Associated With Key Parasite Functions.

Intraspecific differences in biological traits between Neospora caninum isolates have been widely described and associated with variations in virulence. However, the molecular basis underlying these differences has been poorly studied. We demonstrated previously that Nc-Spain7 and Nc-Spain1H, high- and low-virulence isolates, respectively, show different invasion, proliferation and survival capabilities in bovine macrophages (boMØs), a key cell in the immune response against Neospora, and modulate the cell immune response in different ways. Here, we demonstrate that these differences are related to specific tachyzoite gene expression profiles. Specifically, the low-virulence Nc-Spain1H isolate showed enhanced expression of genes encoding for surface antigens and genes related to the bradyzoite stage. Among the primary up-regulated genes in Nc-Spain7, genes involved in parasite growth and redox homeostasis are particularly noteworthy because of their correlation with the enhanced proliferation and survival rates of Nc-Spain7 in boMØs relative to Nc-Spain1H. Genes potentially implicated in induction of proinflammatory immune responses were found to be up-regulated in the low-virulence isolate, whereas the high-virulence isolate showed enhanced expression of genes that may be involved in immune evasion. These results represent a further step in understanding the parasite effector molecules that may be associated to virulence and thus to disease traits as abortion and transmission.

Ecophysiological differences between vesicomyid species and metabolic capabilities of their symbionts influence distribution patterns of the deep‐sea clams

AbstractThis study provides an analysis of vesicomyid bivalve–symbiont community distribution across cold seep and hydrothermal vent areas in the Guaymas Basin (Gulf of California, Mexico). Using a combination of morphological and molecular approaches including fluorescent in situ hybridization (FISH), and electronic microscopy observations, vesicomyid clam species and their associated symbionts were characterized and results were analyzed in light of geochemical conditions and other on‐site observations. A greater diversity of vesicomyids was found at cold seep areas, where three different species were present (Phreagena soyoae [syn. kilmeri], Archivesica gigas, and Calyptogena pacifica). In contrast, A. gigas was the only species sampled across the hydrothermal vent area. The same haplotype of A. gigas was found in both hydrothermal vent and cold seep areas, highlighting possible contemporary exchanges among neighboring vents and seeps. In either ecosystem, molecular characterization of the symbionts confirmed the specificity between symbionts and hosts and supported the hypothesis of a predominantly vertical transmission. In addition, patterns of clams could reflect potential niche preferences for each species. The occurrence of numerous traces of vesicomyid movements on sediments in the sites colonized by A. gigas seemed to indicate that this species might have a better ability to move. Furthermore, variation in gill sulfur content could reveal a higher plasticity and sulfur storage capacity in A. gigas. Thus, the distribution of vesicomyid species across the chemosynthetic areas of the Guaymas Basin could be explained by differences in biological traits of the vesicomyid species that would allow A. gigas to more easily exploit transient and punctual sources of available sulfide than P. soyoae.

Uncovered variability in olive moth (Prays oleae) questions species monophyly.

The olive moth -Prays oleae Bern.- remains a significant pest of olive trees showing situation dependent changes in population densities and in severity of damages. The genetic variability of olive moth was assessed on three main olive orchards regions in Portugal by three different markers (COI, nad5 and RpS5), suggesting high species diversity albeit with no obvious relation with a regional pattern nor to an identified ecological niche. Selected COI sequences obtained in this study were combined with those available in the databases for Prays genus to generate a global dataset. The reconstruction of the Prays phylogeny based on this marker revealed the need to revise Prays oleae to confirm its status of single species: COI data suggests the co-existence of two sympatric evolutionary lineages of morphologically cryptic olive moth. We show, however, that the distinct mitochondrial subdivision observed in the partial COI gene fragment is not corroborated by the other DNA sequences. There is the need of understanding this paradigm and the extent of Prays variability, as the disclosure of lineage-specific differences in biological traits between the identified lineages is fundamental for the development of appropriate pest management practices.

Genetic comparison of the red shrimp Pleoticus muelleri (Decapoda: Solenoceridae) using the barcode gene reveals the absence of cryptic speciation along its distribution

Differences in biological traits (abundance, longevity, size at the onset of sexual maturity, and maximum size) appearing in populations of Pleoticus muelleri from the Western Atlantic are currently considered as phenotypic plasticity. However, they may also be related to intraspecific genetic differentiation and to the occurrence of cryptic speciation. Thus, to assess the genetic diversity and population structure of P. muelleri along its distribution range, we compared cytochrome c oxidase subunit I (COI; the barcode gene) and 16S sequences of individuals from seven localities from the southeastern coast of Brazil and Argentina. Ten polymorphic sites were observed in eleven COI haplotypes, but only one polymorphic site was observed in two 16S haplotypes. The haplotype network, maximum likelihood phylogram, and analyses of molecular variance (AMOVA) indicated the absence of genetic structure between populations, which in turn, points to the absence of cryptic speciation. Therefore, the known phenotypic variations may be indeed a consequence of different environmental conditions.

A revision of the Encarsia pergandiella species complex (Hymenoptera: Aphelinidae) shows cryptic diversity in parasitoids of whitefly pests

AbstractEncarsia pergandiella Howard, described from North America (USA), and Encarsia tabacivora Viggiani, described from South America (Brazil) (Hymenoptera: Aphelinidae), are two formally recognized taxonomic entities, that have been treated by several authors as synonyms due to lack of strong diagnostic characters. Taxonomy of these species is further complicated because several populations, geographically separated and differing in their biology, have been included under the concept of E. pergandiella. Among these, a population originally collected in Brazil and introduced to North America reproduces by thelytokous parthenogenesis and is infected by the symbiont Cardinium, while a morphologically indistinguishable population, naturally occurring in Texas, is biparental and infected by a related strain of Cardinium that induces cytoplasmic incompatibility. A third population known from California and introduced to the Old World is biparental and uninfected by intracellular symbionts. While adult females of the first two populations have entirely light yellow bodies and pupate face up (light form), those of the third population have largely brown bodies and pupate face down (dark form). Other dark form populations are known from Texas, Florida and New York. Because these parasitoids are economically important biological control agents of cosmopolitan whitefly pests, it is critical to characterize them correctly. In this study, we integrated molecular and morphometric analyses to substantiate observed differences in biological traits, and resolve the complicated taxonomy of this species complex. We sequenced the mitochondrial cytochrome c oxidase subunit I gene and the D2 region of the ribosomal 28S gene for individuals of both light form (from Texas and Brazil) and dark form (from California, Texas, Italy and Canary Islands) originating from laboratory cultures or collected in the field. Phylogenetic analysis unambiguously distinguished three well‐supported groups corresponding to the Texas light form, the Brazil light form and the dark form. Individuals of these three groups, in combination with all available type material (E. pergandiella, its synonym Encarsia versicolor Girault and E. tabacivora) and additional museum specimens of the dark form from New York and Italy, were subjected to multivariate morphometric analyses using Burnaby principal component analysis followed by a linear discriminant analysis, and multivariate ratio analysis. Overall, the analyses showed that: (i) E. pergandiella and E. tabacivora are two distinct species; (ii) the thelytokous Brazil light form corresponds to E. tabacivora; (iii) the biparental Texas light form is a new species formally described here as Encarsia suzannae sp.n.; (iv) two new biparental species can be referred to the dark form, one described as Encarsia gennaroi sp.n. including the populations sampled in California, Texas, Italy and Canary Islands, and the other corresponding to the population from New York described as Encarsia marthae sp.n. A dichotomous key for both sexes of the species of the E. pergandiella complex is provided for identification.This published work has been registered in ZooBank, http://zoobank.org/urn:lsid:zoobank.org:pub:278475A0‐C2C4‐4400‐A042‐A5716457829D.

Changes in biological traits of macro-benthic communities subjected to different intensities of demersal trawling along the west coast of southern Africa

Biological traits analysis (BTA) is considered to be a powerful technique for describing the ecological functioning of marine benthic assemblages. This study is the first to apply BTA to assess differences in the traits of benthic faunal assemblages between areas exposed to heavy and light trawling in a major upwelling ecosystem along the west coast of southern Africa. The data were collected from two sampling locations in Namibia and six sampling locations in South Africa. The intensity of trawling varied from area to area. Significant differences in biological traits (BT) were detected between heavily and lightly trawled areas. Weighted infaunal traits showed significant differences between heavily and lightly trawled areas for 17% of the traits investigated, while 24% of epifaunal traits investigated were significantly different between areas of different trawling intensities. This suggests that the measured BTs of the epifauna might be more sensitive to trawling disturbances than BTs of the infauna. The infaunal traits differed significantly between areas with larger or smaller proportions of sand and mud. Nevertheless, more of the significant differences in infaunal BTs were related to variations in trawling intensity than to variations in sediment composition. Significant modifications of BTs are likely to lead to modified functioning of the community and provide more general potential indicators for management than those based on species. The study confirms the need for more basic biological and life history data on macro-benthic invertebrates but nevertheless shows that BTA detected specific features that correlate with trawling intensity and that these features may be important for epifaunal assemblage functioning.

Characterization and Comparative Profiling of miRNAs in Invasive Bemisia tabaci (Gennadius) B and Q

BackgroundMicroRNAs (miRNAs) are small, conserved, non-coding RNAs that post-transcriptionally regulate gene expression. Bemisia tabaci (Gennadius) B and Q are two invasive and dominant whiteflies, and B. tabaci Q has been displacing B in China. Differences in biological traits (fecundity, host range, resistance to insecticides, etc.) as affected by miRNAs might be involved in the displacement. In this study, we performed high-throughput sequencing to identify miRNAs in B. tabaci B and Q.ResultsWe identified 170 conserved miRNAs and 15 novel candidates, and found significant differences in the expression of miRNAs between B. tabaci B and Q.ConclusionExpression levels of miRNAs differ in B. tabaci B vs. Q. Additional research is needed to determine whether these differences are related to differences in the biology of B. tabaci B and Q, and whether these differences help explain why B. tabaci Q is displacing B in China.

A Comprehensive Analysis of Genetic Diversity and Relationships of 13 Sweet Sorghum Varieties as Energy Sources

To investigate the genetic diversity and relationships among the sweet sorghum varieties as energy sources currently bred in China, 13 sweet sorghum varieties were selected for comprehensive analysis through observations of 31 biological traits and examinations of RAPD and SSR molecular markers. The numerical analysis showed that the differences in biological traits existed among 13 varieties, and the genetic distance (DIST) ranged from 0.787 to 2.221, and the two varieties from Inner Mongolia and Xinjiang were distinctly separated from all other varieties. A total of 22 polymorphism primers were obtained from the screening using RAPD marker analysis. The polymorphism rate was 58.33%, and the genetic similarity (GS) coefficients among the studied cultivars ranged from 0.694 to 0.896. Cluster analysis results indicated that the three varieties from Inner Mongolia, Xinjiang and Heilongjiang exhibited significant genetic differences from the other varieties. SSR marker analysis using 31 selected pairs of polymorphic primers showed that the polymorphism rate of amplified fragments was 78.64%, and GS coefficients among the tested cultivars were 0.534 to 0.971. Cluster analysis showed that variety No. 12 from Xinjiang and variety No. 7 from Inner Mongolia clustered into one group, and variety No. 6 from Heilongjiang was in a single group. The other ten varieties were grouped into another separate cluster. The results based on combined data displayed a similar trend with results from the three individual data analyses, but could more comprehensively and objectively reflect the fundamental genetic differences among these varieties. In summary, certain genetic differences exist among the varieties tested from different regions or different breeding institutions. However, varieties from the same region, especially those from the same breeding institution, exhibited small genetic variations and high genetic similarities. At present, more attention should be paid to discovery and innovation in the breeding of sweet sorghum varieties.

Performance of four Trichogramma species (Hymenoptera: Trichogrammatidae) as biocontrol agents of Heliothis virescens (Lepidoptera: Noctuidae) under various temperature regimes

Trichogramma spp. are major parasitoids of lepidopteran pest eggs, but there is large variation in efficacy toward a given pest among the numerous described Trichogramma species. It is important to select the Trichogramma species that most effectively parasitize and develop in target pest eggs for biological control. In this context, Trichogramma pretiosum, T. exiguum, T. atopovirilia and T. acacioi were studied in Heliothis virescens eggs under different thermal conditions. The parasitoids were reared at constant temperatures of 20, 25 and 30°C and tested at these respective temperatures, while parasitoids reared at 25°C were also tested at 20 and 30°C, for a total of 20 species–temperature combinations. About 30 H. virescens eggs were offered to the parasitoids for 24 h. Among the four species, parasitism rate by T. atopovirilia was highest at all temperature conditions, whereas T. acacioi had the lowest rates of parasitism at 25°C and 25/30°C. Parasitism ranged from 13.8 to 43.8% among all species–temperature combinations. Viability (emerged parasitoids) ranged from 80.8 to 98.4%, and was deemed satisfactory. The emergence rates of T. exiguum and T. acacioi were affected by temperature. Temperature also affected the sex ratio of T. exiguum at 25/30°C, whereas T. pretiosum and T. acacioi produced females predominantly independent of temperature. Overall, the parasitoid T. atopovirilia was the most efficient in parasitizing H. virescens eggs, though the levels of parasitism obtained might not ensure its successful use in biological control programs. The temperature-related differences in biological traits observed in the four Trichogramma species tested hint at the importance of making careful choices regarding climatic conditions where the parasitoid is going to be used when selecting a species for biological control programs.

Temperature-dependent differences in biological traits between two strains of Trichogramma cacoeciae (Hymenoptera: Trichogrammatidae)

Parasitoids’ efficiency in controlling pests depends not only on their ability to parasitize their hosts but also on how much they are adapted to climatic conditions (notably temperature) of the area where they are planned to be released. In addition, the optimal conditions for production of parasitoids used for inundative releases like Trichogramma spp. may also vary largely as a function of strains. Using the parasitoid Trichogramma cacoeciae Marchal as biological model, we studied how temperature affects important parasitoid efficiency-related biological traits under laboratory conditions. Emergence, mortality rates and fecundity of two strains of T. cacoeciae, one originating from France (Alsace) and the other one from Tunisia (Degache), were compared at constant temperatures of 15, 20, 25 and 30°C. The parasitoids of the French strain showed highest fecundity at 25°C with wasps that had been reared at 20 or 25°C. The Tunisian strain showed the highest fecundity at 25°C, but only when wasps were previously reared at 25 or 30°C. For both strains, the highest mortality occurred among wasps that had laid eggs at 30°C. Emergence rates were relatively high at all temperatures, although the French strain did better at 15–25°C and the Tunisian one at 20–30°C. Because of the differences in biological traits of these two T.cacoeciae strains in relation to the temperature, a judicious choice must be made among the various strains when using this species in biological control programs.

Genome comparison using Gene Ontology (GO) with statistical testing.

BackgroundAutomated comparison of complete sets of genes encoded in two genomes can provide insight on the genetic basis of differences in biological traits between species. Gene ontology (GO) is used as a common vocabulary to annotate genes for comparison. Current approaches calculate the fold of unweighted or weighted differences between two species at the high-level GO functional categories. However, to ensure the reliability of the differences detected, it is important to evaluate their statistical significance. It is also useful to search for differences at all levels of GO.ResultsWe propose a statistical approach to find reliable differences between the complete sets of genes encoded in two genomes at all levels of GO. The genes are first assigned GO terms from BLAST searches against genes with known GO assignments, and for each GO term the abundance of genes in the two genomes is compared using a chi-squared test followed by false discovery rate (FDR) correction. We applied this method to find statistically significant differences between two cyanobacteria, Synechocystis sp. PCC6803 and Anabaena sp. PCC7120. We then studied how the set of identified differences vary when different BLAST cutoffs are used. We also studied how the results vary when only subsets of the genes were used in the comparison of human vs. mouse and that of Saccharomyces cerevisiae vs. Schizosaccharomyces pombe.ConclusionThere is a surprising lack of statistical approaches for comparing complete genomes at all levels of GO. With the rapid increase of the number of sequenced genomes, we hope that the approach we proposed and tested can make valuable contribution to comparative genomics.

Commensalism, adaptation and gene flow: mosquitoes of the Culex pipiens complex in different habitats.

Two ecotypes have been described for Culex pipiens mosquitoes of the temperate zone: a human commensal type and a feral type, but their degree of evolutionary differentiation and taxonomic status are still unclear. The commensal form is characterized by life-history traits probably adaptive to underground man-made environments. This situation has sometimes been considered as an example of recent speciation although the existence of intermediate forms indicates that the balance between gene flow and disruptive selection should first be assessed. The present study was concerned with (1) the determination of biological traits involved in adaptation to commensalism, and (2) the pattern of gene flow within and between ecotypes in a restricted area. It was found that (1) significant differences in biological traits exist between mosquitoes from different habitats, (2) characteristics of the commensal type are not universal in mosquitoes from underground man-made habitats, (3) allozyme markers do not clearly differentiate ecotypes and (4) insecticide resistance genes, which reveal recent migration, occur in each ecotype. These results are discussed in the context of possible speciation due to commensalism.