Sequence divergence at mitochondrial genes in animals: applicability of DNA data in genetics of speciation and molecular phylogenetics

Nucleotide diversity estimates for the genes Cyt-b (cytochrome b) and Co-1 (cytochrome oxidase 1) are analyzed. Genetic divergence of populations (1) and taxa of different rank, such as subspecies, semispecies or/and sibling species (2), species within a genus (3), species from different genera within a family (4), and species from separate families within an order (5) have been compared using a database of p-distances and similar measures. Empirical data for 20,731 vertebrate and invertebrate animal species reveal various and increasing levels of genetic divergence of the sequences of the two genes, Cyt-b and Co-1, in the five groups compared. Mean unweighted scores of p-distances (%) for five groups are: Cyt-b (1) 1.38±0.30, (2) 5.10±0.91, (3) 10.31±0.93, (4) 17.86±1.36, (5) 26.36±3.88 and Co-1 (1) 0.89±0.16, (2) 3.78±1.18, (3) 11.06±0.53, (4) 16.60±0.69, (5) 20.57±0.40. These estimates testify to the applicability of p-distance for most intraspecies and interspecies comparisons of genetic divergence up to the order level for the two genes compared. The results of the analysis of the nucleotide divergence within species and higher taxa of animals suggest that a phyletic evolution in animals is likely to prevail at the molecular level, and speciation mainly corresponds to the geographic or divergence mode (type D1). The prevalence of the D1 speciation mode does not mean that other modes are absent. At least seven possible modes of speciation are considered. The approach suggested that allows recognize the speciation modes formally with the operational genetic criteria. Such approach may help to solve a key problem of the biological species concept, i.e. the lack of ability to monitor in most cases the reproductive isolation barriers between species.     

Fruit size and shape: Allometry at different taxonomic levels in bird-dispersed plants

Summary The likelihood that a plant's seeds will be dispersed by fruit-eating birds may depend upon the size and shape of its fruits. Assuming that elongate fruits can be swallowed more easily than spherical fruits of equal volume and that plant fitness is enhanced by seed dispersal by many individuals and species of birds, natural selection should favour increasing fruit elongation with increasing fruit size in bird-dispersed plants. According to this view, this allometric pattern would be adaptive. Alternatively, fruit shape in bird-dispersed plants may be constrained by development or phylogeny. To determine whether there was any evidence to support the adaptive allometry hypothesis, we examined allometric relationships between length and diameter in fruits and seeds in a group of neotropical bird-dispersed plant species. Using the major axis technique, we regressed ln(diameter) on ln(length) for fruits and seeds at various taxonomic levels: (1) within individual trees ofOcotea tenera (Lauraceae) (2) among 19 trees within a population ofO. tenera, as well as among pooled fruits from multiple trees within 20 other species in the Lauraceae, (3) among 25 sympatric species within a plant family (Lauraceae) and (4) among 167 species representing 63 angiosperm families within a plant community in Monteverde, Costa Rica. At most taxonomic levels, a tendency for fruit length to increase more rapidly than fruit diameter among fruits (negative allometry) occurred more frequently than expected by chance. Estimated slopes of the regressions of fruit length on fruit diameter were < 1 within 15 of the 19 individualO. tenera trees, among tree means withinO. tenera, among pooled fruits within 16 of the 20 other species in the Lauraceae, among species means within the Lauraceae and among means of all bird-dispersed species in the lower montane forests of Monteverde. Seed allometry showed similar patterns, although for both fruits and seeds the broad confidence intervals of the slopes estimated by major axis regression overlapped 1 in many cases. Among the 63 Monteverde family means, fruit length and diameter scaled isometrically. Based on measurements of ontogenetic changes in fruit shape in a single species,O. viridifolia, we found no evidence that negative allometry in fruit shape within the Lauraceae was an inevitable consequence of developmental constraints. Instead, increasing elongation of fruits and seeds in certain plant taxa is consistent with adaptation to gape-limited avian seed dispersers. Contrary results from vertebrate-dispersed species from Malawi and Spain may reflect differences between the New and Old World in plant taxa, seed dispersers or evolutionary history.     

Early embryogenesis in discoglossoid frogs: a study of heterochrony at different taxonomic levels

We studied the timing of the early development of the cranial neural crest, neural tube differentiation, somite formation and body elongation in the closely related frog species Discoglossus montalenti , Discoglossus galganoi , Discoglossus pictus , Bombina orientalis , Bombina variegata and Bombina maxima . Despite their different egg and embryo sizes, event pairing shows that there are only very few heterochronies among the three Bombina species and the three Discoglossus species in early developmental events. Instead, differences become apparent at the genus level (interpreted as phylogenetic signal). For example, the separation into a mandibular and a hyoid portion of cranial neural crest could be seen earlier in the Discoglossus than in the Bombina species when compared with the development of the neural tube. The development of the cranial neural crest streams also shifts (relatively) forward in time when compared with body elongation and somite formation in the Discoglossus species in contrast to the Bombina species. Comparisons with other species show that attempts to correlate heterochronies in early development with life history changes should take into account the possibility of a rather high evolvability, i.e. a high probability of convergence in the timing of these early events.     

Responses to fish predation and nutrients by plankton at different levels of taxonomic resolution

1. To improve mechanistic understanding of plankton responses to eutrophication, a mesocosm experiment was performed in the shallow littoral zone of a south Swedish lake, in which nutrient and fish gradients were crossed in a fully factorial design. 2. Food chain theory accurately predicted total biomass development of both phyto‐ and zooplankton. However, separating zooplankton and algae into finer taxonomic groups revealed a variety of responses to both nutrient and fish gradients. 3. That both nutrients and fish are important for phytoplankton dynamics was seen more clearly when viewing each algal group separately, than drawing conclusions only from broad system variables such as chlorophyll a concentration or total phytoplankton biovolume. 4. In some taxa, physiological constraints (e.g. sensitivity to high pH and low concentrations of free CO₂) and differences in competitive ability may be more important for the biomass development than fish predation, grazing by herbivorous zooplankton, and nutrient availability. 5. We conclude that food chain theory accurately predicted responses in system variables, such as total zooplankton or algal biomass, which are shaped by the dynamics of certain strong interactors (‘keystone species’), such as large cladocerans, cyanobacteria and edible algae (<50 μm), whereas responses at finer taxonomic levels cannot be predicted from current theory.     

Cope's Rule in the Pterosauria, and differing perceptions of Cope's Rule at different taxonomic levels

The remarkable extinct flying reptiles, the pterosaurs, show increasing body size over 100 million years of the Late Jurassic and Cretaceous, and this seems to be a rare example of a driven trend to large size (Cope's Rule). The size increases continue throughout the long time span, and small forms disappear as larger pterosaurs evolve. Mean wingspan increases through time. Examining for Cope's Rule at a variety of taxonomic levels reveals varying trends within the Pterosauria as a whole, as pterodactyloid pterosaurs increase in size at all levels of examination, but rhamphorhynchoid pterosaurs show both size increase and size decrease in different analyses. These results suggest that analyses testing for Cope's Rule at a single taxonomic level may give misleading results.     

Divergence of TERMINAL FLOWER1-like genes in Rosaceae

Rosaceae is a large family, however, our understanding of its phylogeny is based largely on morphological observations. To understand the relationship between subfamilies Rosoideae, Amygdaloideae, Maloideae and Spiraeoideae at a molecular level, we isolated and compared the plant phosphatidyl ethanolamine-binding protein-like genes TERMINAL FLOWER1 (TFL1)-like and CENTRORADIALIS (CEN)-like, which are involved in the control of shoot meristem identity and flowering time. A comparison of gene structures and phylogenetic tree analyses by the Neighbor-Joining method showed that each of the two TFL1-like (MdTFL1-1 and MdTFL1-2) and CEN-like genes (MdCENa and MdCENb) in Maloideae were classified into two distinct clades. The TFL1-like and CEN-like genes of Gillenia in Spiraeoideae belonged to monophyletic Maloideae groups, suggesting that Gillenia and Maloideae have a common near ancestor. However, the Gillenia TFL1-like gene does not contain the insertion sequence of the third intron that is found in MdTFL1-2-like genes of the members of Maloideae such as apple, Korean whitebeam, quince, and Siberian mountain ash. Therefore, after the Maloideae ancestor genome became polyploid through hybridization between Gillenia-like species or genome doubling, an insertion sequence of the third intron of MdTFL1-2-like genes was generated.     

Occurrence and properties of low molecular weight RNA components from cells at different taxonomic levels.

1. The occurrence and gel electrophoretic properties of low molecular weight RNA components (LMW RNA) have been studied in species at different taxonomic levels. The LMW RNA components apart from tRNA, 5S RNA and 5.5S RNA are called LMW*RNA. 2. The major components of LMW*RNA in mammalian cells are L, A, C and D, accounting for 0.1-0.7% of cellular RNA. The gel electrophoretic migration of components L, C, and D is similar in different mammals but the migration of component A shows differences. 3. Amphibia, reptiles and birds contain L, A, C and D in about the same amounts as mammals but slight differences in migration are seen for L, C and D. Component A is absent from the nucleated red blood cells of the chicken and the frog. 4. Sea urchins contain three LMW*RNA components with migrations different from L, A, C and D. These components account for about 0.1% of the cellular RNA. 5. Insects contain only one LMW*RNA component, migrating as component L. 6. Tetrahymena, Physarum and Mycoplasmas have one component which may be a counterpart to component L in higher cells. Yeast shows no LMW*RNA components. 7. In the multicellular species the occurrence and gel electrophoretic migration of LMW*RNA components are not related to tumorigenicity, developmental stage or origin of tissue.     

Divergence and reproductive isolation in the early stages of speciation

To understand speciation we need to identify the factors causing divergence between natural populations. The traditional approach to gaining such insights has been to focus on a particular theory and ask whether observed patterns of reproductive isolation between populations or species are consistent with the hypothesis in question. However, such studies are few and they do not allow us to compare between hypotheses, so often we cannot determine the relative contribution to divergence of different potential factors. Here, I describe a study of patterns of phenotypic divergence and premating and postmating isolation between populations of the grasshopper Chorthippus parallelus. Information on the phylogeographic relationships of the populations means that a priori predictions from existing hypotheses for the evolution of reproductive isolation can be compared with observations. I assess the relative contributions to premating isolation, postmating isolation and phenotypic divergence of long periods of allopatry, adaptation to different environments and processes associated with colonisation (such as population bottlenecks). Likelihood analysis reveals that long periods of allopatry in glacial refugia are associated with postmating reproductive isolation, but not premating isolation, which is more strongly associated with colonisation. Neither premating nor postmating isolation is higher between populations differing in potential environmental selection pressures. There are only weak correlations between patterns of genetic divergence and phenotypic divergence and no correlation between premating and postmating isolation. This suggests that the potential of a taxon to exercise mate choice may affect the types of factor that promote speciation in that group. I discuss the advantages and disadvantages of the general approach of simultaneously testing competing hypotheses for the evolution of reproductive isolation.     

Ecology and genetics of speciation in Ficedula flycatchers

Birds have for long been popular study objects in speciation research. Being easy to observe in the field, they have traditionally been particularly important in studies of behavioural and ecological factors in speciation, whereas the genetic aspects of the process have been studied in other organisms, such as Drosophila. More recently, however, a stronger genetic focus has been placed on speciation research also in birds. Here, we review ecological, behavioural and genetic studies on speciation in the pied flycatcher (Ficedula hypoleuca) and the collared flycatcher (Ficedula albicollis). These well‐studied birds provide among the few proposed examples of the process of reinforcement of premating isolation, and the evidence for reinforcement is strong. They are further characterized by having strong intrinsic postzygotic barriers (female hybrid sterility), yet the two species appear to be very similar ecologically. This is in stark contrast to another well‐studied bird complex, Darwin’s finches, in which the species differ vastly in ecologically important traits but have no developmental problems arising from genetic incompatibilities, and where no evidence for reinforcement is found. In the flycatchers, sex chromosome linkage of genes affecting traits associated with both pre‐ and postzygotic barriers to gene exchange is likely to facilitate reinforcement. We discuss whether such sex‐linkage may be common in birds. The contrast between flycatchers and Darwin’s finches indicate that speciation in birds cannot always be understood mainly as a result of divergent natural selection (‘ecological speciation’), and generalizations from one system may lead us astray. We discuss to what extent insight from research on the flycatchers may point to fruitful avenues for future research on bird speciation and specifically call for a more systematic effort to simultaneously investigate ecology, behaviour and genetics of birds caught in the process of speciation.     

Sensory drive speciation and patterns of variation at selectively neutral genes

Speciation by sensory drive can occur if divergent adaptation of sensory systems causes rapid evolution of mating traits and the resulting development of assortative mating. Previous theoretical studies have shown that sensory drive can cause rapid divergent adaptive evolution from one to two phenotypes. In this study, we examined two topics: the possibility of adaptive radiation by sensory drive from one to more than two phenotypes and the relationships of patterns of variation at selectively neutral genes to levels of viability selection, habitat and mating preferences and migration. We conducted individual-based simulations assuming a sensory trait and a mating trait controlled by a small number of loci. We found that adaptive radiation is possible when the number of loci controlling the sensory trait is small; the levels of viability selection, habitat and mating preferences are intermediate; and the emigration rate is high. We also found that emigration rates as well as the levels of habitat and mating preferences are related to F _ST values at neutral loci, but F _ST proved to be insensitive to a small change in the number of loci controlling the mating trait. This suggests that an estimation of the past population history is possible without an accurate genetic model.     

The elevational gradient of Andean plant endemism: varying influences of taxon-specific traits and topography at different taxonomic levels

Aim Little is known about the elevational gradient of plant endemism. It is mostly assumed that patterns are determined by topographical factors such as area of elevational belts and degree of habitat fragmentation, but comparative studies of different plant taxa along the same elevational gradient are lacking. The aim was to compare the elevational patterns of plant endemism of the entire flora and selected families and genera in a search for commonalities. Methods The elevational patterns of endemism for the entire Ecuadorean vascular plant flora, for twenty‐seven selected families, and for twenty‐four selected genera based on the Catalogue of Vascular Plants of Ecuador were analysed. Results Elevational patterns of endemism were non‐random at all taxonomic levels but there was no common elevational pattern. Rather, the study groups showed a wide variety of independent patterns at all taxonomic levels. Most groups had hump‐shaped patterns with maxima at different elevations and mostly at the same or at higher elevations than the maxima of species richness. The overall flora showed highest endemism in the narrowest and most fragmented elevational belts, presumably because of the consequent fragmentation of species populations. Main conclusions Patterns of endemism appear to be influenced both by taxon‐specific ecological traits (e.g. life form, reproduction, dispersal, demography, spatial population structure, competitive ability) in their specific interaction with historical processes and by environmental factors such as topographical fragmentation. The degree to which these influences become visible along the elevational gradient are determined by which combination of species is analysed: for a given genus or family, taxon‐specific traits dominate the patterns, for the entire flora taxon‐specific patterns are blurred by averaging and the signal of topography emerges. Beyond the elevational gradient as such, this study shows that the frequently stated assumption that given biogeographical settings lead to similar patterns of endemism among different taxa is wrong.     

The genetics of speciation: genes of small effect underlie sexual isolation in the Hawaiian cricket Laupala

Sexual behaviours often evolve rapidly and are critical for sexual isolation. We suggest that coordinated sexual signals and preferences generate stabilizing selection, favouring the accumulation of many small‐effect mutations in sexual communication traits. Rapid radiation of a sexual behaviour used in signalling, song pulse rate, has been observed in the Hawaiian cricket genus Laupala. Using marker‐assisted introgression, we isolated five known quantitative trait loci (QTL) influencing species‐level differences in pulse rate from one species, L. paranigra, into a closely related species, L. kohalensis. All five QTL were found to have a significant effect on song and appear to be largely additive in backcross introgression lines. Furthermore, all effect sizes were small in magnitude. Our data provide support for the hypothesis that stabilizing selection on sexual signals in Laupala creates genetic conditions favourable to incremental divergence during speciation, through the evolution of alleles of minor rather than major phenotypic effects.     

Phylogenetic utility of 141 low-copy nuclear regions in taxa at different taxonomic levels in two distantly related families of rosids

Angiosperm systematics has progressed to the point where it is now expected that multiple, independent markers be used in phylogenetic studies. Universal primers for amplifying informative regions of the chloroplast genome are readily available, but in the faster-evolving nuclear genome it is challenging to discover priming sites that are conserved across distantly related taxa. With goals including the identification of informative markers in rosids, and perhaps other angiosperms, we screened 141 nuclear primer combinations for phylogenetic utility in two distinct groups of rosids at different taxonomic levels-Psiguria (Cucurbitaceae) and Geraniaceae. We discovered three phylogenetically informative regions in Psiguria and two in Geraniaceae, but none that were useful in both groups. Extending beyond rosids, we combined our findings with those of another recent effort testing these primer pairs in Asteraceae, Brassicaceae, and Orchidaceae. From this comparison, we identified 32 primer combinations that amplified regions in representative species of at least two of the five distantly related angiosperm families, giving some prior indication about phylogenetic usefulness of these markers in other flowering plants. This reduced set of primer pairs for amplifying low-copy nuclear markers along with a recommended experimental strategy provide a framework for identifying phylogenetically informative regions in angiosperms.     

Social learning in animals: comparative analysis of different forms and levels

Social learning as one of the key concepts of cognitive ecology includes different forms of behavioural displays from relatively simple, such as "social release" and "stimulus enhancement" up to "teaching" and "cultural transmission" in animal communities. Rapid development of this fields resulted in some contradictions in methods and terminology. In this review different forms and levels of social learning are analyzed. Ecological aspects of social learning are connected with diet shaping, fear of predators and mate choice. The first aspect is the most studied but still discussible. Social learning being an intricate component of feeding behaviour matches with innate behaviour, imprinting as well as early associative learning. Investigation of cognitive aspects of social learning going back to Thorndike's crucial question "Do apes ape?" are now developing into series of questions including even: "Do ants ape?". Elaboration of universal methods of comparative studying of social learning such as "artificial fruit" and "two ways/one outcome" has essentially enlightened these questions and made comparative analysis possible. Large continuum of displays of cognitive skills in social learning has been revealed in non-primate species. One of the discussible issues in the role of social learning is distribution of innovations. Many authors have investigated this intriguing aspect of animal behaviour in different ways, such as long field observations as well as laboratory experiments based on "artificial innovators" that is specimens specially taught by experimentalists. Many impressive results were obtained; in particular it turned out in contradiction with some mathematical models that individuals in groups are rather different in their psychophysiological predisposition to innovative behaviour. Role of teaching in such different forms of behaviour as shaping of species-specific behavioural patterns and spread of innovations is considered. Although the majority of animals in wild populations are not good teachers and pupils, some cultural aspects of behaviour were recently revealed, mostly in primates. At the same time some classical results concerning cultural transmission of new patterns (for example, bottle-opening in tits) were experimentally revised. Many problems still remain unsolved, in particular, how spread of innovations may favour prosperity of populations; to what degree behavioural peculiarities of local groups may be determined by processes of social learning; which internal and external factors and under what circumstances invest into social learning in natural environment.     

Sensitivity of different taxonomic levels of soil Gamasina to land use and anthropogenic disturbances

• 1 The effect of taxonomic level on the sensitivity of bioindicators has been widely investigated in aquatic ecosystems and, to a lesser extent, in terrestrial ecosystems. However, no studies have been conducted on the sensitivity of the different taxonomic levels of soil mites, especially Gamasina, to human activities.
• 2 The present study aimed to assess the sensitivity of different taxonomic levels of soil Gamasina mites to anthropogenic disturbances in Europe and Argentina. We arranged the data from previous projects in a hierarchical system and conducted a study to identify the critical taxonomical levels that had the highest discriminative potential between sites (Europe and Argentina) or management types (forests, grasslands, fallows, succession, recultivation and agricultural sites).
• 3 For the Gamasina community, geographical location was by far more important than the influence of any land use type. The analysis including only the European sites demonstrated that communities belonging to sites subjected to different land uses were also significantly different.
• 4 The species data set provided a clearer separation of sites according to both the geographical and the land‐use gradients than the genus and family data sets. The genus and, to a lesser extent, the family approach may be sufficient to elucidate the influence of great geographical differences and also of certain land uses (e.g. grasslands from the forests and arable sites).
• 5 Species presence/absence data provided valuable information in our analyses, although the use of quantitative data yielded a clearer separation of sites.

     

Unravelling the drivers of aquatic communities using disparate organismal groups and different taxonomic levels

Bioassessment and monitoring methods should be as cost-efficient as possible. Limiting the number of sites is not a practical solution to face the financial challenges related to bioassessment. Hence, it is highly important to find inexpensive ways to assess and monitor human-impacted environments. Suggestions have been made to use coarser taxonomic levels because they require less expertise and time, or to use single surrogate taxonomic groups that indicate the overall state of ecosystems. In this study, we examined the level of within-taxon and cross-taxon congruence of aquatic bacterial, diatom and macroinvertebrate communities, while simultaneously assessing the chemical, physical and spatial drivers of community structure in these organismal groups. Our study area was an extensively sampled large lake system with high connectivity between sites. Thus, we ensured that spatial processes, if they existed, were well portrayed in our data. Our aim was to find out the taxonomic levels sufficient for the purposes of bioassessment and to detect possible surrogate taxonomic groups. We found that bacterial communities were best associated with pure effects of water chemistry, whereas diatom and macroinvertebrate communities were varyingly related to chemical, physical and spatial variables. Macroinvertebrates were the only group related to small-scale spatial variables, while bacteria and diatoms were associated with variables illustrating spatial relations among sites at large and intermediate scales. Overall, the three organismal groups were mainly related to different chemical parameters. Also, the three organismal groups showed only weak, if any, congruent patterns in their community structure. Thus, we do not recommend the use of only one biological group as a surrogate in bioassessment. However, we found that higher taxonomic levels of all three studied organismal groups could be used as surrogates for finer-level taxonomic assignments. Our findings are promising for the possible use of bacteria in future bioassessment and monitoring. Owing to the characteristics of very large lake systems, our findings may be applied to similarly highly connected ecosystems, such as marine coastal systems.