Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species

With millions of species and their life-stage transformations, the animal kingdom provides a challenging target for taxonomy. Recent work has suggested that a DNA-based identification system, founded on the mitochondrial gene, cytochrome c oxidase subunit 1 (COI), can aid the resolution of this diversity. While past work has validated the ability of COI sequences to diagnose species in certain taxonomic groups, the present study extends these analyses across the animal kingdom. The results indicate that sequence divergences at COI regularly enable the discrimination of closely allied species in all animal phyla except the Cnidaria. This success in species diagnosis reflects both the high rates of sequence change at COI in most animal groups and constraints on intraspecific mitochondrial DNA divergence arising, at least in part, through selective sweeps mediated via interactions with the nuclear genome.     

Inverting the null-hypothesis of speciation: a marine snail perspective

Speciation is currently an intensely debated topic, much more so than 20–30 years ago when most biologists held the view that new species (at least of animals) were formed through the split of evolutionary lineages by the appearance of physical barriers to gene flow. Recent advances have, however, lent both theoretical and empirical support to speciation in the presence of gene flow. Nevertheless, the allopatric hypothesis of speciation is still the default model. The consequence of this is that to support sympatric and parapatric modes of speciation all allopatric alternatives must be rejected, while an allopatric explanation is usually accepted without rejecting possible non-allopatric alternatives. However, classical cases of allopatric speciation can be challenged by alternative non-allopatric explanations, and this begs for a more respectful view of how to deal with all models of speciation. An appealing approach is studying parallel evolution of reproductive barriers, which allows for comparative approaches to distinguish between allopatric and non-allopatric events, and explicit tests of a suitable null-hypothesis. Parallel evolution of reproductive isolation in a strongly polymorphic marine snail species serves as an illustrative example of such an approach. In conclusion, a more balanced debate on allopatric and non-allopatric speciation is needed and an urgent issue is to treat both allopatric and nonallopatric hypotheses critically, rather than using allopatry as the default model of speciation.     

Genetic basis of hybrid male sterility among three closely related species of Drosophila

The genetic basis of hybrid male sterility among three closely related species, Drosophila bipectinata, D. parabipectinata and D. malerkotliana has been investigated by using backcross analysis methods. The role of Y chromosome, major hybrid sterility (MHS) genes (genetic factors) and cytoplasm (non-genetic factor) have been studied in the hybrids of these three species. In the species pair, bipectinata--parabipectinata, Y chromosome introgression of parabipectinata in the genomic background of bipectinata and the reciprocal Y chromosome introgression were unsuccessful as all males in second backcross generation were sterile. Neither MHS genes nor cytoplasm was found important for sterility. This suggests the involvement of X-Y, X-autosomes or polygenic interactions in hybrid male sterility. In bipectinata--malerkotliana and parabipectinata--malerkotliana species pairs, Y chromosome substitution in reciprocal crosses did not affect male fertility. Backcross analyses also show no involvement of MHS genes or cytoplasm in hybrid male sterility in these two species pairs. Therefore, X- autosome interaction or polygenic interaction is supposed to be involved in hybrid male sterility in these two species pairs. These findings also provide evidence that even in closely related species, genetic interactions underlying hybrid male sterility may vary.     

The unusual inheritance pattern of the courtship songs in closely related grasshopper species of the Chorthippus albomarginatus-group (Orthoptera: Gomphocerinae)

Sibling species of the Chorthippus albomarginatus-group are exceptional among all European grasshopper species because they have an extremely elaborate courtship behaviour. Here, we present a genetic analysis of the courtship song differences between two closely related grasshopper species Ch. albomarginatus and Ch. oschei. Measurements of seven courtship song characters and one parameter of courtship visual display were compared among parentals, F(1) and F(2) hybrids, and backcrosses. Variation in one morphological character, the number of stridulatory pegs, was studied as well. The distributions of song phenotypes were more consistent with a type-III genetic architecture, which involves complementary or duplicate pairs of loci. We suggest that this type of architecture may provide the novel elements of the hybrid songs, even more complex than the parental ones, which may offer a new starting point for sexual selection. One parameter of the visual display appeared to be controlled by a single locus, but differences in other characters of visual display could be explained by a more complex inheritance pattern. Inheritance of the peg number differences was consistent with a simple polygenic additive model. Sex linkage and/or maternal effects were not detected for any trait. We found a disproportionate influence of the Ch. albomarginatus parent on most hybrid song characteristics and the visual display, and this may support a previously suggested idea that Ch. albomarginatus is an ancestral form and Ch. oschei is a derived species.     

DNA reassociation kinetics of closely related species

The kinetics of reassociation of the DNA of three groups of closely related organisms were examined. The laboratory mouse was compared to an Asiatic mouse, whose chromosome number is the same but whose chromosome organization is different. Chinese hamster (2N=22) was compared to Syrian hamster (2N=44), and Haplopappus gracilis (2N=4) was compared to H. ravenit (2N=8). It was found that the most highly repeated DNA fractions of the three comparative sets of organisms differ in their reaction rates. However, these fractions of the related hamsters, haplopappi, and probably the mice, do not differ in the amount of DNA composing the fractions. The intermediately fast reassociating DNA and the unique DNA do not differ between members of related pairs of organisms. The implication of these results is that a short sequence of DNA may be highly copied in one organism, while in a related organism a longer DNA sequence is repeated a fewer number of times, and the total amount of repeated DNA may be the same in both related organisms.     

Strong differences in chemical recognition cues between two closely related species of ants from the genus Lasius (Hymenoptera: Formicidae)

Cuticular hydrocarbons (CHCs) are increasingly recognized as important to insects and are used for constructing taxonomies. However, multiple parameters affect the expression of CHCs besides a genetic component. We propose that selection may act differently on the expression of CHCs, depending on the evolutionary context. To explore the influence of selection, the CHCs of two closely related ant species, Lasius niger and Lasius platythorax, were studied in a multidisciplinary approach. We characterized (i) CHCs and (ii) niches (through baiting, activity observations and foraging analysis). The species were distinct in both measures, although to a varying degree. Although they showed moderate niche partitioning along diet and environmental preferences, chemical differences were unexpectedly pronounced. This may be explained by divergent selection on mate recognition cues or by other influences on CHCs. Such striking chemical differences among closely related species may not be the rule and suggest that taxonomies based on CHCs should be interpreted cautiously; though, they remain useful tools for differentiating among cryptic species.     

Typing of four genetic loci discriminates among closely related species of New World Leishmania

All New World Leishmania species can cause cutaneous lesions, while only Leishmania (Viannia) braziliensis has been associated with mucosal metastases. Multilocus enzyme electrophoresis (MLEE) is the optimal standard for species identification but is slow and costly. New methods for species identification are needed to ensure proper identification and therapy. The coding regions of four metabolic enzyme markers in the MLEE typing method: mannose phosphate isomerase (MPI), malate dehydrogenase (MDH), glucose-6-phosphate isomerase (GPI), and 6-phosphogluconate dehydrogenase (6PGD), were analysed from seven species of New World Leishmania isolated from patients with either cutaneous or mucosal lesions to identify specific genetic polymorphisms responsible for the phenotypic variations observed in the MLEE typing scheme. We identified species-specific polymorphisms and determined that a combination of sequencing of the mpi and 6pgd genes was sufficient to differentiate among seven closely related species of New World Leishmania and among isolates of L. braziliensis shown previously to have atypical MLEE patterns. When DNA isolated from 10 cutaneous lesion biopsies were evaluated, the sequence typing method was 100% concordant with the published MLEE/monoclonal antibody identification methods. The identification of species-specific polymorphisms can be used to design a DNA-based test with greater discriminatory power that requires shorter identification times. When the causative agent of the disease is L. braziliensis, this method ensures correct species identification, even when the agent is a genetic variant. Proper identification could facilitate adequate treatment, preventing the onset of the disfiguring mucosal form of the disease.     

The geographical pattern of speciation and floral diversification in the neotropics: the tribe sinningieae (gesneriaceae) as a case study

The geographical pattern of speciation and the relationship between floral variation and species ranges were investigated in the tribe Sinningieae (Gesneriaceae), which is found mainly in the Atlantic forests of Brazil. Geographical distribution data recorded on a grid system of 0.5 x 0.5 degree intervals and a near-complete species-level phylogenetic tree of Sinningieae inferred from a simultaneous analysis of seven DNA regions were used to address the role of geographical isolation in speciation. Geographical range overlaps between sister lineages were measured across all nodes in the phylogenetic tree and analyzed in relation to relative ages estimated from branch lengths. Although there are several cases of species sympatry in Sinningieae, patterns of sympatry between sister taxa support the predominance of allopatric speciation. The pattern of sympatry between sister taxa is consistent with range shifts following allopatric speciation, except in one clade, in which the overlapping distribution of recent sister species indicates speciation within a restricted geographical area and involving changes in pollinators and habitats. The relationship between floral divergence and regional sympatry was also examined by analyzing floral contrasts, phenological overlap, and the degree of sympatry between sister clades. Morphological contrast between flowers is not increased in sympatry and phenological divergence is more apparent between allopatric clades than between sympatric clades. Therefore, our results failed to indicate a tendency for sympatric taxa to minimize morphological and phenological overlap (geographic exclusion and/or character displacement hypotheses). Instead, they point toward adaptation in phenology to local conditions and buildup of sympatries at random with respect to flower morphology. Additional studies at a lower geographical scale are needed to identify truely coexisting species and the components of their reproductive isolation.     

Quantitative analysis of gametic incompatibility between closely related species of neotropical sea urchins

Species of the sea urchin genus Echinometra found on the two coasts of Panamá are recently diverged and only partially isolated by incomplete barriers to interspecific fertilization. This study confirms previous work that revealed incompatibility between the eggs of the Atlantic E. lucunter and the sperm of the other two neotropical species, whereas eggs of its sympatric congener E. viridis and allopatric E. vanbrunti are largely compatible with heterospecific sperm. Here we quantify fertilization using a range of sperm dilutions. We demonstrate a much stronger block to cross-species fertilization of E. lucunter eggs than was previously shown at fixed sperm concentrations, and mild incompatibility of the other two species' eggs where previous crosses between species were not distinguishable from within-species controls. Additionally, we present evidence for intraspecific variation in egg receptivity towards heterospecific sperm. Our findings here again discount the "reinforcement model" as a viable explanation for the pattern of prezygotic isolation. Gamete incompatibility in these Echinometra has appeared recently-within the last 1.5 million years-but is weaker in sympatry than in allopatry. Accidents of history may help explain why incompatibility of eggs emerged in one species and not in others. Compensatory sexual selection on sperm in this species could follow, and promote divergence of proteins mediating sperm-egg recognition.     

Genetic analysis of incompatibility in the diploid Ipomoea species closely related to the sweet potato

Summary In order to identify the genotypic constitutions of incompatibility in the diploid species, Ipomoea leucantha Jacq. (K221), which is most closely related to the sweet potato, the progenies derived from the reciprocal crosses, backcrosses and testcrosses were analysed. All the plants examined were self-incompatible, and pollen germination was inhibited on the stigma after incompatible pollinations. No reciprocal differences were found in the incompatibility reactions. In the progenies three incompatibility groups were observed which showed the rather simple segregation ratios. The homozygous plants for incompatibility alleles were obtained in the progenies. The experimental results demonstrated a sporophytic type of incompatibility controlled by a single locus with multiple S-alleles exhibiting a dominance relationship in both the pollen and the stigma. The plants obtained in the progenies had the following genotypes: S ₁ S ₂, S ₁ S ₃, S ₂ S ₂, S ₂ S ₃ and S ₃ S ₃.     

The systematics of Porphyra: character evolution in closely related species

Isozymes, vegetative and reproductive morphology, seasonality, vertical and geographic distributions and chromosomes were compared for six pairs of putative sibling species of Porphyra (P. abbottae/P. torta, P. fallax subsp. fallax/P. fallax subsp. conwayae, P. amplissima/P. cuneiformis, P. fucicola/P. leucostica, P. miniata/P. variegata, P. umbilicalis/P. umbilicalis) and among five species in a complex (P. brumalis, P. kurogii, P. linearis, P. pseudolinearis, and P. purpurea.) Geographic distribution and zymograms for certain proteins showed the greatest change between species pairs: only one pair of species had identical distributions, and most species pairs were disjunct; every species had a different allozyme for GOT-1, whereas all species had apparently identical proteins for phycoerythrin. Seasonality and habitat exhibited moderate differentiation: Northeast Pacific sibling species were characterized by a high intertidal winter species pairing with a mid intertidal spring species, whereas all but one of the other species pairs exhibited nearly identical vertical distributions and seasonalities. There were few changes in morphology: most species pairs had essentially identical morphologies and coloration and the same arrangement of reproductive cells. Chromosome numbers and karyotypes were identical for species pairs and in the species complex. These results provide evidence for different rates of evolution of different characters in the genus Porphyra.     

Regional divergence and mosaic spatial distribution of two closely related damselfly species (Enallagma hageni and Enallagma ebrium)

North American Enallagma damselflies radiated during the Pleistocene, and species differ mainly by reproductive structures. Although morphologically very different, Enallagma hageni and Enallagma ebrium are genetically very similar. Partitioning of genetic variation (AFLP), isolation by distance and clustering analyses indicate that these morphospecies are locally differentiated genetically. Spatial analyses show that they are rarely sympatric at local sites, and their distributions form a mosaic of patches where one is clearly dominant over hundreds of square kilometers. However, these morphospecies are also not genetically more similar when they are sympatric, indicating that hybridization is probably not occurring. Given that these morphospecies are ecologically equivalent, strong assortative mating, reproductive interference and fast post-glacial recolonization may explain the origin and maintenance of these distributional patches across eastern North America. By limiting opportunities for gene flow, reproductive interference may play an unsuspected role in accelerating genetic differentiation in the early phases of nonecological speciation.     

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.     

New species and new records of recently described species of the coral genus Acropora (Scleractinia: Astrocoeniina: Acroporidae) from Indonesia

Six new species of the coral genus Acropora arc described from Indonesia. These include a species which is remarkable for tubercular cocnostcal structures similar to those of the confamilial genus Montipora. The new species include three regional endemics (A. togianensis and A. batunai from central east Sulawesi and A. derawanensis from east Kalimantan), one species with broad distribution across the southern island chains (A. sukarnoi) and two species which occur throughout most of the Indonesian archipelago (A. Indonesia and A. hoeksemai). A further two species described from Western Australia and Papua New Guinea in 1994 (A. turaki and A. jacquelineae respectively) are recorded from Indonesia for the first time, as common members of an unusual assemblage type in the Togian Islands. The range of another species described from Lombok in 1994 (A. suharsonoi) is extended into Bali. With A. desalwii, A. lokani and A. indiana , this brings to 12 the number of Acropora species newly recorded as being endemic to the Indonesian archipelago or to Indonesia and one adjoining region (either the Indian Ocean or the western Pacific).