Interspecific Substitution Research Articles

Latitudinal trends in the structure, similarity and beta diversity of plant communities invaded by Alternanthera philoxeroides in heterogeneous habitats.

Variations in latitudinal gradients could lead to changes in the performance and ecological effects of invasive plants and thus may affect the species composition, distribution and interspecific substitution of native plant communities. However, variations in structure, similarity and beta (β) diversity within invaded communities across latitudinal gradients in heterogeneous habitats remain unclear. In this study, we conducted a two-year field survey along 21°N to 37°N in China, to examine the differential effects of the amphibious invasive plant Alternanthera philoxeroides on native plant communities in terrestrial and aquatic habitats. We compared the differences in the invasion importance value (IV), species distribution, community similarity (Jaccard index and Sorenson index) and β diversity (Bray−Curtis index and βsim index) between terrestrial and aquatic communities invaded by A. philoxeroides, as well as analyzed their latitudinal trends. We found that the IV of A. philoxeroides and β diversity in aquatic habitats were all significantly higher than that of terrestrial, while the terrestrial habitat had a higher community similarity values. The aquatic A. philoxeroides IV increased with increasing latitude, while the terrestrial IV had no significant latitudinal trend. With increasing latitude, the component proportion of cold- and drought-tolerant species in the terrestrial communities increased, and the dominant accompanying species in the aquatic communities gradually changed from hygrophytes and floating plants to emerged and submerged plants. In addition, the aquatic communities had lower community similarity values and higher β diversity in higher latitudinal regions, while terrestrial communities had the opposite parameters in these regions. Our study indicates that the bioresistance capacities of the native communities to invasive A. philoxeroides in heterogeneous habitats are different; A. philoxeroides invasion leads to higher community homogenization in terrestrial habitats than in aquatic habitats, and terrestrial communities experience more severe homogenization in higher latitudinal regions. These findings are crucial for predicting the dynamics of invasive plant communities under rapid global change.

Worldwide molecular phylogeny of common estuarine polychaetes of the genus Hediste (Annelida: Nereididae), with special reference to interspecific common haplotypes found in southern Japan

The nucleotide sequences of two mitochondrial genes (16S rDNA and COI) were compared among all species of Hediste, including five nominal and two cryptic species (H. atoka and H. diversicolor both consisting of two cryptic species, H. diadroma, H. japonica, and H. limnicola), as well as a newly found undescribed species (H. sp.), to estimate their phylogenetic relationships. The analysis using 16S rDNA sequence supported the monophyly of all five nominal species and H. sp., with no detection of the genetic differentiation between the two cryptic species in both H. atoka and H. diversicolor. However, analysis using COI sequence detected a marked differentiation between the cryptic species, and indicated that the two forms of H. atoka were separated into distinct clades; form A was included in a clade together with H. diversicolor, H. limnicola, and H. sp., whereas form B was included in another clade together with H. diadroma. Based on the topology of our phylogenetic analysis using the combined data set of 16S rDNA and COI, a hypothesis on the evolutionary history of the worldwide speciation in Hediste is proposed. This hypothesis seems to correspond well with the geographical distributions of current species and their morphological differentiation, supporting the previous hypothesis that the unique epitokous swarming and planktic larval development evolved independently in H. diadroma and H. japonica in eastern Asia. We also show that no or few interspecific substitutions have occurred in sequences of nuclear DNA (18S rDNA, 28S rDNA, and histone H3) in Hediste.

Structural dynamics flexibility informs function and evolution at a proteome scale

Protein structures are dynamic entities with a myriad of atomic fluctuations, side-chain rotations, and collective domain movements. Although the importance of these dynamics to proper functioning of proteins is emerging in the studies of many protein families, there is a lack of broad evidence for the critical role of protein dynamics in shaping the biological functions of a substantial fraction of residues for a large number of proteins in the human proteome. Here, we propose a novel dynamic flexibility index (dfi) to quantify the dynamic properties of individual residues in any protein and use it to assess the importance of protein dynamics in 100 human proteins. Our analyses involving functionally critical positions, disease-associated and putatively neutral population variations, and the rate of interspecific substitutions per residue produce concordant patterns at a proteome scale. They establish that the preservation of dynamic properties of residues in a protein structure is critical for maintaining the protein/biological function. Therefore, structural dynamics needs to become a major component of the analysis of protein function and evolution. Such analyses will be facilitated by the dfi, which will also enable the integrative use of structural dynamics with evolutionary conservation in genomic medicine as well as functional genomics investigations.

A PCR‐Based Method to Distinguish the Sibling Species Stylonychia mytilus and Stylonychia lemnae (Ciliophora, Spirotrichea) Using Isocitrate Dehydrogenase Gene Sequences

A differentiation, based on morphological characters, between Stylonychia mytilus and Stylonychia lemnae is very difficult, especially for non-specialists. These two sibling species were considered as one species, S. mytilus, until detailed cytological and genetic studies could show the existence of two genetically isolated varieties. Further morphological and biochemical analyses verified the separation and finally in 1983 a new species S. lemnae was described. The examination of several isoenzymes revealed unambiguous differences in the banding pattern of isocitrate dehydrogenase (IDH) between these two species. Therefore, the IDH gene of 30 isolates of S. lemnae and S. mytilus coming from various regions all over the world were amplified and sequenced. The sequence analyses revealed intraspecific as well as interspecific substitutions, which were used for the development of species-specific PCR primers for both species. Application of these species-specific primer pairs now allows a very easy and clear identification of both sibling species.

Amount of introgression in flycatcher hybrid zones reflects regional differences in pre and post‐zygotic barriers to gene exchange

Introgression is the incorporation of alleles from one species or semispecies into the gene pool of another through hybridization and backcrossing. The rate at which this occurs depends on the frequency of hybridization and the fitness of hybrids and backcrosses compared to 'pure' individuals. The collared flycatcher (Ficedula albicollis) and the pied flycatcher (F. hypoleuca) co-exist and hybridize at low to moderate frequencies in a clinal hybrid zone in Central Europe and on the islands of Gotland and Oland off the Swedish east coast. Data on hatching success suggest that hybrids are less fertile in Central Europe compared to on the islands. Direct fitness estimates using molecular markers to infer paternity are consistent with the demographic data. Applying a tag-array-based minisequencing assay to genotype interspecific substitutions and single nucleotide polymorphisms we demonstrate that the amount of introgression from the pied to the collared flycatcher is higher in the two island populations (Gotland and Oland) than in two geographically distinct areas from the Central European hybrid zone (Czech Republic and Hungary). In all areas the amount of introgression from collared to pied flycatchers is very low or seemingly absent. The different patterns of introgression are consistent with regional differences in rates of hybridization and fitness of hybrids. We suggest that barriers to gene exchange may have been partly broken down on the islands due to asymmetric gene flow from allopatry. Alternatively, or in addition, more pronounced reinforcement of prezygotic isolation in Central Europe might have increased post-zygotic isolation through hitchhiking, since genes affecting pre and post-zygotic isolation are both sex-linked in these birds. One of our genetic markers appears to introgress from pied to collared flycatchers at a much higher rate than the other markers. We discuss the possibility that the introgressed marker may be linked to a gene which is under positive selection in the novel genetic background.

Sex chromosome evolution and speciation in Ficedula flycatchers.

Speciation is the combination of evolutionary processes that leads to the reproductive isolation of different populations. We investigate the significance of sex-chromosome evolution on the development of post- and prezygotic isolation in two naturally hybridizing Ficedula flycatcher species. Applying a tag-array-based mini-sequencing assay to genotype single nucleotide polymorphisms (SNPs) and interspecific substitutions, we demonstrate rather extensive hybridization and backcrossing in sympatry. However, gene flow across the partial postzygotic barrier (introgression) is almost exclusively restricted to autosomal loci, suggesting strong selection against introgression of sex-linked genes. In addition to this partial postzygotic barrier, character displacement of male plumage characteristics has previously been shown to reinforce prezygotic isolation in these birds. We show that male plumage traits involved in reinforcing prezygotic isolation are sex linked. These results suggest a major role of sex-chromosome evolution in mediating post- and prezygotic barriers to gene flow and point to a causal link in the development of the two forms of reproductive isolation.

Control of the limb bud outgrowth in quail-chick chimera.

It is well known that the apical ectodermal ridge (AER) and the zone of polarizing activity (ZPA) play a major role in growth and patterning of the limb. But a mechanism underlying species-specific growth of the limb has not yet been fully elucidated. To investigate the role of AER and ZPA in limb size control, we constructed quail-chick limb chimeras. When we grafted a whole forelimb bud from one species to another, the size of the developed grafted limb was comparable to the limb of the donor species. Moreover, we demonstrated that neither the interspecific substitution of the posterior half region of the limb bud containing the ZPA nor the exchange of the ectodermal component of the limb involving the AER could alter the species-specific size of the limb. These results indicate that the factors affecting the size of the limb are already involved in the mesodermal component of the limb bud at stage 20 of chick embryo. Thus, the mesoderm dictates limb specificity including size.

Control of the limb bud outgrowth in quail‐chick chimera

It is well known that the apical ectodermal ridge (AER) and the zone of polarizing activity (ZPA) play a major role in growth and patterning of the limb. But a mechanism underlying species-specific growth of the limb has not yet been fully elucidated. To investigate the role of AER and ZPA in limb size control, we constructed quail-chick limb chimeras. When we grafted a whole forelimb bud from one species to another, the size of the developed grafted limb was comparable to the limb of the donor species. Moreover, we demonstrated that neither the interspecific substitution of the posterior half region of the limb bud containing the ZPA nor the exchange of the ectodermal component of the limb involving the AER could alter the species-specific size of the limb. These results indicate that the factors affecting the size of the limb are already involved in the mesodermal component of the limb bud at stage 20 of chick embryo. Thus, the mesoderm dictates limb specificity including size. Dev Dyn 208:85–91, 1997. © 1997 Wiley-Liss, Inc.

Ecosystem configurations consequent on the maximum respiration hypothesis

The Maximum Respiration Hypothesis (MRH) asserts that matured ecosystems organize their configuration to maximize community respiration. Hence the object of the hypothesis is not individual living organisms but the whole ecosystem. In this paper we use two types of ecosystem models to show how the MRH works in ecosystems. The first is a simple theoretical model that consists of two compartments: a producer and a decomposer. The main results of this first model are as follows. (1) The model presents the community structure which is consistent with the MRH. (2) The dual solution (respiration values) presents the scarcities of different types of matter and energy in an ecosystem with maximal respiration. They operate as similar indicators to the inverse of buffer capacity. (3) The model, when extended to include two types of decomposers, can show the conditions of the coexistence and the competitive exclusion of components. Even if two biological components are strongly overlapping in their ecological niches, a slight differentiation of the ratio of matter exchanges can permit the coexistence. The competition and the coexistence are regulated by the imperative shown by the MRH. The second model is a simulation model for a hypothetical grassland ecosystem which consists of 19 biological components, and 15 kinds of matter and energy. The model includes a grazer system and a decomposer system. The main results are as follows. (1) The ecosystem configuration for biomass production, consumption, egestion, nutrient production, and respiration is presented under the MRH. It especially shows the dominance of the decomposer system. (2) Interspecific substitution guided by respiration values cause an increase in community respiration. If an inferior component undergoes a mutation to increase its production of net respiration value, the component may dominate its competitor and contribute to the increase in the community respiration. This means that the MRH can predict the working of natural selection from the macroscopic point of view.

A new source of cytoplasmic male sterility in sunflower

Interspecific substitutions of the nucleus of Helianthus annuus (2n=34) cv. Saturn into the cytoplasm of H. petiolaris (2n=34) by successive backcrossing, resulted in progenies with indehiscent anthers containing white, rather than normal yellow, pollen. Further backcrossing by cv. Saturn failed to restore pollen shed, suggesting that the male sterility was cytoplasmic. In vivo germination tests of pollen from 23 such plants from eight BC5 lines, indicated complete pollen sterility for 14 plants, but normal seed set, suggesting that female fertility was not affected. Meiosis in all plants examined was normal.

Interspecific hybrids between helianthus PetiolarisNutt. and H. Annuus L.: Effect of backcrossing on meiosis

Interspecific substitutions of the nucleus of Helianthus annuus (2n=34) into the cytoplasm of H. petiolaris (2n=34) were obtained by successive backcrossing using cultivated sunflower, H. annuus, as the recurrent pollen parent. Meiosis in the F1 was characterized by multivalents, suggesting that 10 of the 34 chromosomes were heterozygous for chromosomal interchanges. An additional pair of chromosomes also contained a paracentric inversion. Continued backcrossing resulted in rapid elimination of the meiotic aberrations evident in the F1. In the BC1, 1 of 11 plants had normal meiosis and by the BC2, only 13 of 54 plants had meiotic aberrations similar to those of the F1. However, trisomic progeny (2n=35) were found in 3 of the 11 BC1 plants and 20 of the 54 BC2 plants. No meiotic aberrations were observed in BC3 or BC4 plants. Plants with indehiscent anthers, and considered to be male sterile (M.S.), first occurred in the BC1 and, by the BC2, 51 of 54 plants were M.S. All 19 BC3 and 16 BC4 plants were M.S. Preliminary investigations suggest that the pollen from such plants is sterile and that the sterility is cytoplasmic rather than genetic. Disc-flower measurements were a useful technique for selecting samples at the correct stage of microsporogenesis, but could not be used to distinguish between successive backcrosses.