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Several recent studies reported on so-called audience effects in male Atlantic mollies (Poecilia mexicana), in which the visual presence of a potential rival affects male sexual activity. We asked whether and how audience effects interact with male sexual harassment. Poecilia mexicana almost constantly attempt to mate, while females are mostly non- responsive to male approaches. Females flee from this sexual harassment and, thus, are more vigilant in the presence of males, so females may have hampered feeding opportunities. Do audience effects lead to altered male sexual harassment? Focal females were given an opportunity to feed in the presence of a male or a female partner and the difference in feeding times was interpreted as an effect caused by male harassment. Tests were conducted without an audience (1), or an audience male was visually presented either directly inside the test tank (2), or further away (in an adjoining compartment (3)). We found that levels of pre-mating behaviour did not vary significantly among treatments, but males exhibited more copulation attempts (thrusting) in treatment (3), suggesting that males respond to increased risk of sperm competition with higher sperm expenditure. Females fed less (and started feeding later) when a harassing partner male was around, and this effect was not dependent on the audience treatment, but, overall, females spent more time feeding (and started feeding earlier) when an audience was presented. Hence, feeding time reductions appear to be independent of audience effects, but perceived 'safety in numbers' may lead to increased foraging in larger groups.
Genetic divergence is impacted by many factors, including phylogenetic history, gene flow, genetic drift, and divergent selection. Rotifers are an important component of aquatic ecosystems, and genetic variation is essential to their ongoing adaptive diversification and local adaptation. In addition to coding sequence divergence, variation in gene expression may relate to variable heat tolerance, and can impose ecological barriers within species. Temperature plays a significant role in aquatic ecosystems by affecting species abundance, spatio-temporal distribution, and habitat colonization. Recently described (formerly cryptic) species of the Brachionus calyciflorus complex exhibit different temperature tolerance both in natural and in laboratory studies, and show that B. calyciflorus sensu stricto (s.s.) is a thermotolerant species. Even within B. calyciflorus s.s., there is a tendency for further temperature specializations. Comparison of expressed genes allows us to assess the impact of stressors on both expression and sequence divergence among disparate populations within a single species. Here, we have used RNA-seq to explore expressed genetic diversity in B. calyciflorus s.s. in two mitochondrial DNA lineages with different phylogenetic histories and differences in thermotolerance. We identify a suite of candidate genes that may underlie local adaptation, with a particular focus on the response to sustained high or low temperatures. We do not find adaptive divergence in established candidate genes for thermal adaptation. Rather, we detect divergent selection among our two lineages in genes related to metabolism (lipid metabolism, metabolism of xenobiotics).
Genetic divergence is impacted by many factors, including phylogenetic history, gene flow, genetic drift, and divergent selection. Rotifers are an important component of aquatic ecosystems, and genetic variation is essential to their ongoing adaptive diversification and local adaptation. In addition to coding sequence divergence, variation in gene expression may relate to variable heat tolerance, and can impose ecological barriers within species. Temperature plays a significant role in aquatic ecosystems by affecting species abundance, spatio-temporal distribution, and habitat colonization. Recently described (formerly cryptic) species of the Brachionus calyciflorus complex exhibit different temperature tolerance both in natural and in laboratory studies, and show that B. calyciflorus sensu stricto (s.s.) is a thermotolerant species. Even within B. calyciflorus s.s., there is a tendency for further temperature specializations. Comparison of expressed genes allows us to assess the impact of stressors on both expression and sequence divergence among disparate populations within a single species. Here, we have used RNA-seq to explore expressed genetic diversity in B. calyciflorus s.s. in two mitochondrial DNA lineages with different phylogenetic histories and differences in thermotolerance. We identify a suite of candidate genes that may underlie local adaptation, with a particular focus on the response to sustained high or low temperatures. We do not find adaptive divergence in established candidate genes for thermal adaptation. Rather, we detect divergent selection among our two lineages in genes related to metabolism (lipid metabolism, metabolism of xenobiotics).
Thermal stress response is an essential physiological trait that determines occurrence and temporal succession in nature, including response to climate change. We compared temperature-related demography in closely related heat-tolerant and heat-sensitive Brachionus rotifer species. We found significant differences in heat response, with the heat-sensitive species adopting a strategy of long survival and low population growth, while the heat-tolerant followed the opposite strategy. In both species, we examined the genetic basis of physiological variation by comparing gene expression across increasing temperatures. Comparative transcriptomic analyses identified shared and opposing responses to heat. Interestingly, expression of heat shock proteins (hsps) was strikingly different in the two species and mirrored differences in population growth rates, showing that hsp genes are likely a key component of a species’ adaptation to different temperatures. Temperature induction caused opposing patterns of expression in further functional categories including energy, carbohydrate and lipid metabolism, and in genes related to ribosomal proteins. In the heat-sensitive species, elevated temperatures caused up-regulation of genes related to meiosis induction and post-translational histone modifications. This work demonstrates the sweeping reorganizations of biological functions that accompany temperature adaptation in these two species and reveals potential molecular mechanisms that might be activated for adaptation to global warming.
Thermal stress response is an essential physiological trait that determines occurrence and temporal succession in nature, including response to climate change. We compared temperature-related demography in closely related heat-tolerant and heat-sensitive Brachionus rotifer species. We found significant differences in heat response, with the heat-sensitive species adopting a strategy of long survival and low population growth, while the heat-tolerant followed the opposite strategy. In both species, we examined the genetic basis of physiological variation by comparing gene expression across increasing temperatures. Comparative transcriptomic analyses identified shared and opposing responses to heat. Interestingly, expression of heat shock proteins (hsps) was strikingly different in the two species and mirrored differences in population growth rates, showing that hsp genes are likely a key component of a species’ adaptation to different temperatures. Temperature induction caused opposing patterns of expression in further functional categories including energy, carbohydrate and lipid metabolism, and in genes related to ribosomal proteins. In the heat-sensitive species, elevated temperatures caused up-regulation of genes related to meiosis induction and post-translational histone modifications. This work demonstrates the sweeping reorganizations of biological functions that accompany temperature adaptation in these two species and reveals potential molecular mechanisms that might be activated for adaptation to global warming.
Under global warming scenarios, rising temperatures can constitute heat stress to which species may respond differentially. Within a described species, knowledge on cryptic diversity is of further relevance, as different lineages/cryptic species may respond differentially to environmental change. The Brachionus calyciflorus species complex (Rotifera), which was recently described using integrative taxonomy, is an essential component of aquatic ecosystems. Here, we tested the hypothesis that these (formerly cryptic) species differ in their heat tolerance. We assigned 47 clones with nuclear ITS1 (nuITS1) and mitochondrial COI (mtCOI) markers to evolutionary lineages, now named B. calyciflorus sensu stricto (s.s.) and B. fernandoi. We selected 15 representative clones and assessed their heat tolerance as a bi-dimensional phenotypic trait affected by both the intensity and duration of heat stress. We found two distinct groups, with B. calyciflorus s.s. clones having higher heat tolerance than the novel species B. fernandoi. This apparent temperature specialization among former cryptic species underscores the necessity of a sound species delimitation and assignment, when organismal responses to environmental changes are investigated.
Predation is a strong species interaction causing severe harm or death to prey. Thus, prey species have evolved various defence strategies to minimize predation risk, which may be immediate (e.g., a change in behaviour) or transgenerational (morphological defence structures). We studied the behaviour of two strains of a rotiferan prey (Brachionus calyciflorus) that differ in their ability to develop morphological defences in response to their predator Asplanchna brightwellii. Using video analysis, we tested: (a) if two strains differ in their response to predator presence and predator cues when both are undefended; (b) whether defended individuals respond to live predators or their cues; and (c) if the morphological defence (large spines) per se has an effect on the swimming behaviour. We found a clear increase in swimming speed for both undefended strains in predator presence. However, the defended specimens responded neither to the predator presence nor to their cues, showing that they behave indifferently to their predator when they are defended. We did not detect an effect of the spines on the swimming behaviour. Our study demonstrates a complex plastic behaviour of the prey, not only in the presence of their predator, but also with respect to their defence status.
Predation is a strong species interaction causing severe harm or death to prey. Thus, prey species have evolved various defence strategies to minimize predation risk, which may be immediate (e.g., a change in behaviour) or transgenerational (morphological defence structures). We studied the behaviour of two strains of a rotiferan prey (Brachionus calyciflorus) that differ in their ability to develop morphological defences in response to their predator Asplanchna brightwellii. Using video analysis, we tested: (a) if two strains differ in their response to predator presence and predator cues when both are undefended; (b) whether defended individuals respond to live predators or their cues; and (c) if the morphological defence (large spines) per se has an effect on the swimming behaviour. We found a clear increase in swimming speed for both undefended strains in predator presence. However, the defended specimens responded neither to the predator presence nor to their cues, showing that they behave indifferently to their predator when they are defended. We did not detect an effect of the spines on the swimming behaviour. Our study demonstrates a complex plastic behaviour of the prey, not only in the presence of their predator, but also with respect to their defence status.
Many animals that have to cope with predation have evolved mechanisms to reduce their predation risk. One of these mechanisms is change in morphology, for example, the development of spines. These spines are induced, when mothers receive chemical signals of a predator (kairomones) and their daughters are then equipped with defensive spines. We studied the behaviour of a prey and its predator when the prey is either defended or undefended. We used common aquatic micro-invertebrates, the rotifers Brachionus calyciflorus (prey) and Asplanchna brightwellii (predator) as experimental animals. We found that undefended prey increased its swimming speed in the presence of the predator. The striking result was that the defended prey did not respond to the predator's presence. This suggests that defended prey has a different response behaviour to a predator than undefended conspecifics. Our study provides further insights into complex zooplankton predator-prey interactions. Predation is a strong species interaction causing severe harm or death to prey. Thus, prey species have evolved various defence strategies to minimize predation risk, which may be immediate (e.g., a change in behaviour) or transgenerational (morphological defence structures). We studied the behaviour of two strains of a rotiferan prey (Brachionus calyciflorus) that differ in their ability to develop morphological defences in response to their predator Asplanchna brightwellii. Using video analysis, we tested: (a) if two strains differ in their response to predator presence and predator cues when both are undefended; (b) whether defended individuals respond to live predators or their cues; and (c) if the morphological defence (large spines) per se has an effect on the swimming behaviour. We found a clear increase in swimming speed for both undefended strains in predator presence. However, the defended specimens responded neither to the predator presence nor to their cues, showing that they behave indifferently to their predator when they are defended. We did not detect an effect of the spines on the swimming behaviour. Our study demonstrates a complex plastic behaviour of the prey, not only in the presence of their predator, but also with respect to their defence status.
Voltage-gated sodium channels, Nav1, play a crucial role in the generation and propagation of action potentials and substantially contribute to the shape of their rising phase. The electric organ discharge (EOD) of African weakly electric fish (Mormyroidea) is the sum of action potentials fired from all electrocytes of the electric organ at the same time and hence voltage-gated sodium channels are one factor—together with the electrocyte’s morphology and innervation pattern—that determines the properties of these EODs. Due to the fish-specific genome duplication, teleost fish possess eight copies of sodium channel genes (SCN), which encode for Nav1 channels. In mormyroids, SCN4aa is solely expressed in the electrocytes of the adult electric organ. In this study, we compared entire SCN4aa sequences of six species of the genus Campylomormyrus and identified nonsynonymous substitutions among them. SCN4aa in Campylomormyrus exhibits a much higher evolutionary rate compared to its paralog SCN4ab, whose expression is not restricted to the electric organ. We also found evidence for strong positive selection on the SCN4aa gene within Mormyridae and along the lineage ancestral to the Mormyridae. We have identified sites at which all nonelectric teleosts are monomorphic in their amino acid, but mormyrids have different amino acids. Our findings confirm the crucial role of SCN4aa in EOD evolution among mormyrid weakly electric fish. The inferred positive selection within Mormyridae makes this gene a prime candidate for further investigation of the divergent evolution of pulse-type EODs among closely related species.
The electric organ (EO) of weakly electric mormyrids consists of flat, disk-shaped electrocytes with distinct anterior and posterior faces. There are multiple species-characteristic patterns in the geometry of the electrocytes and their innervation. To further correlate electric organ discharge (EOD) with EO anatomy, we examined four species of the mormyrid genus Campylomormyrus possessing clearly distinct EODs. In C. compressirostris, C. numenius, and C. tshokwe, all of which display biphasic EODs, the posterior face of the electrocytes forms evaginations merging to a stalk system receiving the innervation. In C. tamandua that emits a triphasic EOD, the small stalks of the electrocyte penetrate the electrocyte anteriorly before merging on the anterior side to receive the innervation. Additional differences in electrocyte anatomy among the former three species with the same EO geometry could be associated with further characteristics of their EODs. Furthermore, in C. numenius, ontogenetic changes in EO anatomy correlate with profound changes in the EOD. In the juvenile the anterior face of the electrocyte is smooth, whereas in the adult it exhibits pronounced surface foldings. This anatomical difference, together with disparities in the degree of stalk furcation, probably contributes to the about 12 times longer EOD in the adult.
Laura Pavesi, Elvira De Matthaeis, Ralph Tiedemann, and Valerio Ketmaier (2011) Temporal population genetics and COI phylogeography of the sandhopper Macarorchestia remyi (Amphipoda: Talitridae). Zoological Studies 50(2): 220-229. In this study we assessed levels of genetic divergence and variability in 208 individuals of the supralittoral sandhopper Macarorchestia remyi, a species strictly associated with rotted wood stranded on sand beaches, by analyzing sequence polymorphisms in a fragment of the mitochondrial DNA (mtDNA) gene coding cytochrome oxidase subunit I (COI). The geographical distribution and ecology of the species are poorly known. The study includes 1 Tyrrhenian and 2 Adriatic populations sampled along the Italian peninsula plus a single individual found on Corfu Is. (Greece). The Tyrrhenian population was sampled monthly for 1 yr. Genetic data revealed a deep phylogeographic break between the Tyrrhenian and Adriatic populations with no shared haplotypes. The single individual collected on Corfu Is. carried the most common haplotype found in the Tyrrhenian population. A mismatch analysis could not reject the hypothesis of a sudden demographic expansion in almost all but 2 monthly samples. When compared to previous genetic data centered on a variety of Mediterranean talitrids, our results place M. remyi among those species with profound intraspecific divergence (sandhoppers) and dissimilar from beachfleas, which generally display little population genetic structuring.
Talitrids are semiterrestrial crustacean amphipods inhabiting sandy and rocky beaches; they generally show limited active dispersal over long distances. In this study we assessed levels of population genetic structure and variability in the talitrid amphipod Orchestia montagui, a species strictly associated to stranded decaying heaps of the seagrass Posidonia oceanica. The study is based on six populations (153 individuals) and covers five basins of the Mediterranean Sea (Tyrrhenian, Ionian, Adriatic, Western and Eastern basins). Samples were screened for polymorphisms at a fragment of the mitochondrial DNA (mtDNA) coding for the cytochrome oxidase subunit I gene (COI; 571 base pairs) and at eight microsatellite loci. MtDNA revealed a relatively homogeneous haplogroup, which clustered together the populations from the Western, Tyrrhenian and Eastern basins, but not the populations from the Adriatic and Ionian ones; microsatellites detected two clusters, one including the Adriatic and Ionian populations, the second grouping all the others. We found a weak geographic pattern in the genetic structuring of the species, with a lack of isolation by distance at either class of markers. Results are discussed in terms of probability of passive dispersal over long distances through heaps of seagrass.
Introduction: We examined patterns of genetic divergence in 26 Mediterranean populations of the semi-terrestrial beachflea Orchestia montagui using mitochondrial (cytochrome oxidase subunit I), microsatellite (eight loci) and allozymic data. The species typically forms large populations within heaps of dead seagrass leaves stranded on beaches at the waterfront. We adopted a hierarchical geographic sampling to unravel population structure in a species living at the sea-land transition and, hence, likely subjected to dramatically contrasting forces.
Results: Mitochondrial DNA showed historical phylogeographic breaks among Adriatic, Ionian and the remaining basins (Tyrrhenian, Western and Eastern Mediterranean Sea) likely caused by the geological and climatic changes of the Pleistocene. Microsatellites (and to a lesser extent allozymes) detected a further subdivision between and within the Western Mediterranean and the Tyrrhenian Sea due to present-day processes. A pattern of isolation by distance was not detected in any of the analyzed data set.
Conclusions: We conclude that the population structure of O. montagui is the result of the interplay of two contrasting forces that act on the species population genetic structure. On one hand, the species semi-terrestrial life style would tend to determine the onset of local differences. On the other hand, these differences are partially counter-balanced by passive movements of migrants via rafting on heaps of dead seagrass leaves across sites by sea surface currents. Approximate Bayesian Computations support dispersal at sea as prevalent over terrestrial regionalism.
Introduction: We examined patterns of genetic divergence in 26 Mediterranean populations of the semi-terrestrial beachflea Orchestia montagui using mitochondrial (cytochrome oxidase subunit I), microsatellite (eight loci) and allozymic data. The species typically forms large populations within heaps of dead seagrass leaves stranded on beaches at the waterfront. We adopted a hierarchical geographic sampling to unravel population structure in a species living at the sea-land transition and, hence, likely subjected to dramatically contrasting forces.
Results: Mitochondrial DNA showed historical phylogeographic breaks among Adriatic, Ionian and the remaining basins (Tyrrhenian, Western and Eastern Mediterranean Sea) likely caused by the geological and climatic changes of the Pleistocene. Microsatellites (and to a lesser extent allozymes) detected a further subdivision between and within the Western Mediterranean and the Tyrrhenian Sea due to present-day processes. A pattern of isolation by distance was not detected in any of the analyzed data set.
Conclusions: We conclude that the population structure of O. montagui is the result of the interplay of two contrasting forces that act on the species population genetic structure. On one hand, the species semi-terrestrial life style would tend to determine the onset of local differences. On the other hand, these differences are partially counter-balanced by passive movements of migrants via rafting on heaps of dead seagrass leaves across sites by sea surface currents. Approximate Bayesian Computations support dispersal at sea as prevalent over terrestrial regionalism.
Background: Local adaptation to divergent environmental conditions can promote population genetic differentiation even in the absence of geographic barriers and hence, lead to speciation. Perturbations by catastrophic events, however, can distort such parapatric ecological speciation processes. Here, we asked whether an exceptionally strong flood led to homogenization of gene pools among locally adapted populations of the Atlantic molly (Poecilia mexicana, Poeciliidae) in the Cueva del Azufre system in southern Mexico, where two strong environmental selection factors (darkness within caves and/or presence of toxic H2S in sulfidic springs) drive the diversification of P. mexicana. Nine nuclear microsatellites as well as heritable female life history traits (both as a proxy for quantitative genetics and for trait divergence) were used as markers to compare genetic differentiation, genetic diversity, and especially population mixing (immigration and emigration) before and after the flood. Results: Habitat type (i.e., non-sulfidic surface, sulfidic surface, or sulfidic cave), but not geographic distance was the major predictor of genetic differentiation. Before and after the flood, each habitat type harbored a genetically distinct population. Only a weak signal of individual dislocation among ecologically divergent habitat types was uncovered (with the exception of slightly increased dislocation from the Cueva del Azufre into the sulfidic creek, El Azufre). By contrast, several lines of evidence are indicative of increased flood-induced dislocation within the same habitat type, e.g., between different cave chambers of the Cueva del Azufre. Conclusions: The virtual absence of individual dislocation among ecologically different habitat types indicates strong natural selection against migrants. Thus, our current study exemplifies that ecological speciation in this and other systems, in which extreme environmental factors drive speciation, may be little affected by temporary perturbations, as adaptations to physico-chemical stressors may directly affect the survival probability in divergent habitat types.
Males often face strong mating competition by neighboring males in their social environment. A recent study by Plath et al. (Anim Behav 75:21-29, 2008a) has demonstrated that the visual presence of a male competitor (i.e., an audience male) affects the expression of male mating preferences in a poeciliid fish (Poecilia mexicana) with a weaker expression of mating preferences when an audience male observed the focal male. This may be a tactic to reduce sperm competition, since surrounding males likely share intrinsic preferences for female traits or copy mate choice decisions. Here, we examined the hypothesis that a same-sex audience would affect female mate preferences less than male mating preferences. Our hypothesis was based on the assumptions that (1) competition for mates in a fashion that would be comparable in strength to sperm competition or overt male-male aggression is absent among Poecilia females, and (2) P. mexicana females typically form female-biased shoals, such that almost any female mate choice in nature occurs in front of a female audience. Poecilia females (P. mexicana, surface and cave form, and the closely related gynogenetic Poecilia formosa) were given a choice between a large and a small male, and the tests were repeated while a conspecific, a heterospecific, or no audience female (control) was presented. Females spent more time in the neutral zone and, thus, less time near the males during the second part of a trial when an audience was presented, but-consistent with predictions-females showed only slightly weaker expression of mate preferences during the second part of the tests. This decline was not specific to the treatment involving an audience and was significantly weaker than the effect seen in the male sex.
Evolutionary relationships of different populations of the threatened malagasy lemur Lepilemur septentrimialis were assessed by sequence analysis of mitochondrial DNA (D-loop region and partial Cyt b gene). One hundred and fifty nine samples were collected from five main different localities in the northern part of Madagascar. We applied the phylogenetic species concept based on fixed diagnostic differences to determine the status of different geographical populations. No nucleotide site diagnoses Ankarana from Andrafiamena or Analamera. However, numerous fixed differences separate Sahafary from all other populations. These results were corroborated by phylogenetic trees. As previous cytogenetic studies, our molecular data suggest that two cryptic species of Lepilemur occur in the extreme north of Madagascar. This speciation is probably caused by chromosomal rearrangements in at least one of the evolutionary lineages. Our study comprises another striking example of how molecular genetic assay can detect phylogenetic discontinuities that are not reflected in traditional morphologically based taxonomies. Our study indicates that the Sahafary population is a hitherto undescribed endangered endemic species which urgently needs conservation efforts. (C) 2003 Elsevier Inc. All rights reserved
Orca (Orcinus orca) strandings are rare and post-mortem examinations on fresh individuals are scarce. Thus, little is known about their parasitological fauna, prevalence of infections, associated pathology and the impact on their health. During post-mortem examinations of two male neonatal orcas stranded in Germany and Norway, lungworm infections were found within the bronchi of both individuals. The nematodes were identified as Halocercus sp. (Pseudaliidae), which have been described in the respiratory tract of multiple odontocete species, but not yet in orcas. The life cycle and transmission pathways of some pseudaliid nematodes are incompletely understood. Lungworm infections in neonatal cetaceans are an unusual finding and thus seem to be an indicator for direct mother-to-calf transmission (transplacental or transmammary) of Halocercus sp. nematodes in orcas.
A challenge for eco-evolutionary research is to better understand the effect of climate and landscape changes on species and their distribution. Populations of species can respond to changes in their environment through local genetic adaptation or plasticity, dispersal, or local extinction. The individual-based modeling (IBM) approach has been repeatedly applied to assess organismic responses to environmental changes. IBMs simulate emerging adaptive behaviors from the basic entities upon which both ecological and evolutionary mechanisms act. The objective of this review is to summarize the state of the art of eco-evolutionary IBMs and to explore to what degree they already address the key responses of organisms to environmental change. In this, we identify promising approaches and potential knowledge gaps in the implementation of eco-evolutionary mechanisms to motivate future research. Using mainly the ISI Web of Science, we reveal that most of the progress in eco-evolutionary IBMs in the last decades was achieved for genetic adaptation to novel local environmental conditions. There is, however, not a single eco-evolutionary IBM addressing the three potential adaptive responses simultaneously. Additionally, IBMs implementing adaptive phenotypic plasticity are rare. Most commonly, plasticity was implemented as random noise or reaction norms. Our review further identifies a current lack of models where plasticity is an evolving trait. Future eco-evolutionary models should consider dispersal and plasticity as evolving traits with their associated costs and benefits. Such an integrated approach could help to identify conditions promoting population persistence depending on the life history strategy of organisms and the environment they experience.
Background
Organisms are expected to respond to changing environmental conditions through local adaptation, range shift or local extinction. The process of local adaptation can occur by genetic changes or phenotypic plasticity, and becomes especially relevant when dispersal abilities or possibilities are somehow constrained. For genetic changes to occur, mutations are the ultimate source of variation and the mutation rate in terms of a mutator locus can be subject to evolutionary change. Recent findings suggest that the evolution of the mutation rate in a sexual species can advance invasion speed and promote adaptation to novel environmental conditions. Following this idea, this work uses an individual-based model approach to investigate if the mutation rate can also evolve in a sexual species experiencing different conditions of directional climate change, under different scenarios of colored stochastic environmental noise, probability of recombination and of beneficial mutations. The color of the noise mimicked investigating the evolutionary dynamics of the mutation rate in different habitats.
Results
The results suggest that the mutation rate in a sexual species experiencing directional climate change scenarios can evolve and reach relatively high values mainly under conditions of complete linkage of the mutator locus and the adaptation locus. In contrast, when they are unlinked, the mutation rate can slightly increase only under scenarios where at least 50% of arising mutations are beneficial and the rate of environmental change is relatively fast. This result is robust under different scenarios of stochastic environmental noise, which supports the observation of no systematic variation in the mutation rate among organisms experiencing different habitats.
Conclusions
Given that 50% beneficial mutations may be an unrealistic assumption, and that recombination is ubiquitous in sexual species, the evolution of an elevated mutation rate in a sexual species experiencing directional climate change might be rather unlikely. Furthermore, when the percentage of beneficial mutations and the population size are small, sexual species (especially multicellular ones) producing few offspring may be expected to react to changing environments not by adaptive genetic change, but mainly through plasticity. Without the ability for a plastic response, such species may become – at least locally – extinct.
Background
Organisms are expected to respond to changing environmental conditions through local adaptation, range shift or local extinction. The process of local adaptation can occur by genetic changes or phenotypic plasticity, and becomes especially relevant when dispersal abilities or possibilities are somehow constrained. For genetic changes to occur, mutations are the ultimate source of variation and the mutation rate in terms of a mutator locus can be subject to evolutionary change. Recent findings suggest that the evolution of the mutation rate in a sexual species can advance invasion speed and promote adaptation to novel environmental conditions. Following this idea, this work uses an individual-based model approach to investigate if the mutation rate can also evolve in a sexual species experiencing different conditions of directional climate change, under different scenarios of colored stochastic environmental noise, probability of recombination and of beneficial mutations. The color of the noise mimicked investigating the evolutionary dynamics of the mutation rate in different habitats.
Results
The results suggest that the mutation rate in a sexual species experiencing directional climate change scenarios can evolve and reach relatively high values mainly under conditions of complete linkage of the mutator locus and the adaptation locus. In contrast, when they are unlinked, the mutation rate can slightly increase only under scenarios where at least 50% of arising mutations are beneficial and the rate of environmental change is relatively fast. This result is robust under different scenarios of stochastic environmental noise, which supports the observation of no systematic variation in the mutation rate among organisms experiencing different habitats.
Conclusions
Given that 50% beneficial mutations may be an unrealistic assumption, and that recombination is ubiquitous in sexual species, the evolution of an elevated mutation rate in a sexual species experiencing directional climate change might be rather unlikely. Furthermore, when the percentage of beneficial mutations and the population size are small, sexual species (especially multicellular ones) producing few offspring may be expected to react to changing environments not by adaptive genetic change, but mainly through plasticity. Without the ability for a plastic response, such species may become – at least locally – extinct.
Populations adapt to novel environmental conditions by genetic changes or phenotypic plasticity. Plastic responses are generally faster and can buffer fitness losses under variable conditions. Plasticity is typically modeled as random noise and linear reaction norms that assume simple one-to- one genotype–phenotype maps and no limits to the phenotypic response. Most studies on plasticity have focused on its effect on population viability. However, it is not clear, whether the advantage of plasticity depends solely on environmental fluctuations or also on the genetic and demographic properties (life histories) of populations. Here we present an individual-based model and study the relative importance of adaptive and nonadaptive plasticity for populations of sexual species with different life histories experiencing directional stochastic climate change. Environmental fluctuations were simulated using differentially autocorrelated climatic stochasticity or noise color, and scenarios of directiona
climate change. Nonadaptive plasticity was simulated as a random environmental effect on trait development, while adaptive plasticity as a linear, saturating, or sinusoidal reaction norm. The last two imposed limits to the plastic response and emphasized flexible interactions of the genotype with the environment. Interestingly, this assumption led to (a) smaller phenotypic than genotypic variance in the population (many-to- one genotype–phenotype map) and the coexistence of polymorphisms, and (b) the maintenance of higher genetic variation—compared to linear reaction norms and genetic determinism—even when the population was exposed to a constant environment for several generations. Limits to plasticity led to genetic accommodation, when costs were negligible, and to the appearance of cryptic variation when limits were exceeded. We found that adaptive plasticity promoted population persistence under red environmental noise and was particularly important for life histories with low fecundity. Populations produing more offspring could cope with environmental fluctuations solely by genetic changes or random plasticity, unless environmental change was too fast.
Populations adapt to novel environmental conditions by genetic changes or phenotypic plasticity. Plastic responses are generally faster and can buffer fitness losses under variable conditions. Plasticity is typically modeled as random noise and linear reaction norms that assume simple one-to- one genotype–phenotype maps and no limits to the phenotypic response. Most studies on plasticity have focused on its effect on population viability. However, it is not clear, whether the advantage of plasticity depends solely on environmental fluctuations or also on the genetic and demographic properties (life histories) of populations. Here we present an individual-based model and study the relative importance of adaptive and nonadaptive plasticity for populations of sexual species with different life histories experiencing directional stochastic climate change. Environmental fluctuations were simulated using differentially autocorrelated climatic stochasticity or noise color, and scenarios of directiona
climate change. Nonadaptive plasticity was simulated as a random environmental effect on trait development, while adaptive plasticity as a linear, saturating, or sinusoidal reaction norm. The last two imposed limits to the plastic response and emphasized flexible interactions of the genotype with the environment. Interestingly, this assumption led to (a) smaller phenotypic than genotypic variance in the population (many-to- one genotype–phenotype map) and the coexistence of polymorphisms, and (b) the maintenance of higher genetic variation—compared to linear reaction norms and genetic determinism—even when the population was exposed to a constant environment for several generations. Limits to plasticity led to genetic accommodation, when costs were negligible, and to the appearance of cryptic variation when limits were exceeded. We found that adaptive plasticity promoted population persistence under red environmental noise and was particularly important for life histories with low fecundity. Populations produing more offspring could cope with environmental fluctuations solely by genetic changes or random plasticity, unless environmental change was too fast.
Background: Although nowaday it is broadly accepted that mitochondrial DNA (mtDNA) may undergo recombination, the frequency of such recombination remains controversial. Its estimation is not straightforward, as recombination under homoplasmy (i.e., among identical mt genomes) is likely to be overlooked. In species with tandem duplications of large mtDNA fragments the detection of recombination can be facilitated, as it can lead to gene conversion among duplicates. Although the mechanisms for concerted evolution in mtDNA are not fully understood yet, recombination rates have been estimated from "one per speciation event" down to 850 years or even "during every replication cycle".
Results: Here we present the first complete mt genome of the avian family Bucerotidae, i.e., that of two Philippine hornbills, Aceros waldeni and Penelopides panini. The mt genomes are characterized by a tandemly duplicated region encompassing part of cytochrome b, 3 tRNAs, NADH6, and the control region. The duplicated fragments are identical to each other except for a short section in domain I and for the length of repeat motifs in domain III of the control region. Due to the heteroplasmy with regard to the number of these repeat motifs, there is some size variation in both genomes; with around 21,657 bp (A. waldeni) and 22,737 bp (P. panini), they significantly exceed the hitherto longest known avian mt genomes, that of the albatrosses. We discovered concerted evolution between the duplicated fragments within individuals. The existence of differences between individuals in coding genes as well as in the control region, which are maintained between duplicates, indicates that recombination apparently occurs frequently, i. e., in every generation.
Conclusions: The homogenised duplicates are interspersed by a short fragment which shows no sign of recombination. We hypothesize that this region corresponds to the so-called Replication Fork Barrier (RFB), which has been described from the chicken mitochondrial genome. As this RFB is supposed to halt replication, it offers a potential mechanistic explanation for frequent recombination in mitochondrial genomes.
Background: Although nowaday it is broadly accepted that mitochondrial DNA (mtDNA) may undergo recombination, the frequency of such recombination remains controversial. Its estimation is not straightforward, as recombination under homoplasmy (i.e., among identical mt genomes) is likely to be overlooked. In species with tandem duplications of large mtDNA fragments the detection of recombination can be facilitated, as it can lead to gene conversion among duplicates. Although the mechanisms for concerted evolution in mtDNA are not fully understood yet, recombination rates have been estimated from "one per speciation event" down to 850 years or even "during every replication cycle".
Results: Here we present the first complete mt genome of the avian family Bucerotidae, i.e., that of two Philippine hornbills, Aceros waldeni and Penelopides panini. The mt genomes are characterized by a tandemly duplicated region encompassing part of cytochrome b, 3 tRNAs, NADH6, and the control region. The duplicated fragments are identical to each other except for a short section in domain I and for the length of repeat motifs in domain III of the control region. Due to the heteroplasmy with regard to the number of these repeat motifs, there is some size variation in both genomes; with around 21,657 bp (A. waldeni) and 22,737 bp (P. panini), they significantly exceed the hitherto longest known avian mt genomes, that of the albatrosses. We discovered concerted evolution between the duplicated fragments within individuals. The existence of differences between individuals in coding genes as well as in the control region, which are maintained between duplicates, indicates that recombination apparently occurs frequently, i. e., in every generation.
Conclusions: The homogenised duplicates are interspersed by a short fragment which shows no sign of recombination. We hypothesize that this region corresponds to the so-called Replication Fork Barrier (RFB), which has been described from the chicken mitochondrial genome. As this RFB is supposed to halt replication, it offers a potential mechanistic explanation for frequent recombination in mitochondrial genomes.
Fourteen microsatellite markers were isolated and characterized for the endangered Visayan tarictic hornbill (Penelopides panini, Aves: Bucerotidae). In an analysis of 76 individuals, the number of alleles per locus varied from one to 12. Expected and observed heterozygosity ranged from 0.00 to 0.87 and from 0.00 to 0.89, respectively. All primers also amplify microsatellite loci in Luzon tarictic hornbill (Penelopides manillae), Mindanao tarictic hornbill (Penelopides affinis), the critically endangered Walden's hornbill (Aceros waldeni) and the near-threatened writhed hornbill (Aceros leucocephalus). Two loci which are monomorphic in P. panini were found polymorphic in at least one of the other species. These 14 new microsatellite markers specifically developed for two genera of Philippine hornbills, in combination with those already available for the hornbill genera Buceros and Bucorvus, comprise a reasonable number of loci to genetically analyse wild and captive populations of these and probably other related, often endangered hornbills.
Background: The Visayan Tarictic Hornbill (Penelopides panini) and the Walden's Hornbill (Aceros waldeni) are two threatened hornbill species endemic to the western islands of the Visayas that constitute - between Luzon and Mindanao - the central island group of the Philippine archipelago. In order to evaluate their genetic diversity and to support efforts towards their conservation, we analyzed genetic variation in similar to 600 base pairs (bp) of the mitochondrial control region I and at 12-19 nuclear microsatellite loci. The sampling covered extant populations, still occurring only on two islands (P. panini: Panay and Negros, A. waldeni: only Panay), and it was augmented with museum specimens of extinct populations from neighboring islands. For comparison, their less endangered (= more abundant) sister taxa, the Luzon Tarictic Hornbill (P. manillae) from the Luzon and Polillo Islands and the Writhed Hornbill (A. leucocephalus) from Mindanao Island, were also included in the study. We reconstructed the population history of the two Penelopides species and assessed the genetic population structure of the remaining wild populations in all four species.
Results: Mitochondrial and nuclear data concordantly show a clear genetic separation according to the island of origin in both Penelopides species, but also unravel sporadic over-water movements between islands. We found evidence that deforestation in the last century influenced these migratory events. Both classes of markers and the comparison to museum specimens reveal a genetic diversity loss in both Visayan hornbill species, P. panini and A. waldeni, as compared to their more abundant relatives. This might have been caused by local extinction of genetically differentiated populations together with the dramatic decline in the abundance of the extant populations.
Conclusions: We demonstrated a loss in genetic diversity of P. panini and A. waldeni as compared to their sister taxa P. manillae and A. leucocephalus. Because of the low potential for gene flow and population exchange across islands, saving of the remaining birds of almost extinct local populations - be it in the wild or in captivity - is particularly important to preserve the species' genetic potential.
Background: The Visayan Tarictic Hornbill (Penelopides panini) and the Walden's Hornbill (Aceros waldeni) are two threatened hornbill species endemic to the western islands of the Visayas that constitute - between Luzon and Mindanao - the central island group of the Philippine archipelago. In order to evaluate their genetic diversity and to support efforts towards their conservation, we analyzed genetic variation in similar to 600 base pairs (bp) of the mitochondrial control region I and at 12-19 nuclear microsatellite loci. The sampling covered extant populations, still occurring only on two islands (P. panini: Panay and Negros, A. waldeni: only Panay), and it was augmented with museum specimens of extinct populations from neighboring islands. For comparison, their less endangered (= more abundant) sister taxa, the Luzon Tarictic Hornbill (P. manillae) from the Luzon and Polillo Islands and the Writhed Hornbill (A. leucocephalus) from Mindanao Island, were also included in the study. We reconstructed the population history of the two Penelopides species and assessed the genetic population structure of the remaining wild populations in all four species.
Results: Mitochondrial and nuclear data concordantly show a clear genetic separation according to the island of origin in both Penelopides species, but also unravel sporadic over-water movements between islands. We found evidence that deforestation in the last century influenced these migratory events. Both classes of markers and the comparison to museum specimens reveal a genetic diversity loss in both Visayan hornbill species, P. panini and A. waldeni, as compared to their more abundant relatives. This might have been caused by local extinction of genetically differentiated populations together with the dramatic decline in the abundance of the extant populations.
Conclusions: We demonstrated a loss in genetic diversity of P. panini and A. waldeni as compared to their sister taxa P. manillae and A. leucocephalus. Because of the low potential for gene flow and population exchange across islands, saving of the remaining birds of almost extinct local populations - be it in the wild or in captivity - is particularly important to preserve the species' genetic potential.
Philippine hornbills of the genera Aceros and Penelopides (Bucerotidae) are known to possess a large tandemly duplicated fragment in their mitochondrial genome, whose paralogous parts largely evolve in concert. In the present study, we surveyed the two distinguishable duplicated control regions in several individuals of the Luzon Tarictic Hornbill Penelopides manillae, compare their characteristics within and across individuals, and report on an intraspecific mitochondrial gene rearrangement found in one single specimen, i.e., an interchange between the two control regions. To our knowledge, this is the first observation of two distinct mitochondrial genome rearrangements within a bird species. We briefly discuss a possible evolutionary mechanism responsible for this pattern, and highlight potential implications for the application of control region sequences as a marker in population genetics and phylogeography.
Background
The unisexual Amazon molly (Poecilia formosa) originated from a hybridization between two sexual species, the sailfin molly (Poecilia latipinna) and the Atlantic molly (Poecilia mexicana). The Amazon molly reproduces clonally via sperm-dependent parthenogenesis (gynogenesis), in which the sperm of closely related species triggers embryogenesis of the apomictic oocytes, but typically does not contribute genetic material to the next generation. We compare for the first time the gonadal transcriptome of the Amazon molly to those of both ancestral species, P. mexicana and P. latipinna.
Results
We sequenced the gonadal transcriptomes of the P. formosa and its parental species P. mexicana and P. latipinna using Illumina RNA-sequencing techniques (paired-end, 100 bp). De novo assembly of about 50 million raw read pairs for each species was performed using Trinity, yielding 106,922 transcripts for P. formosa, 115,175 for P. latipinna, and 133,025 for P. mexicana after eliminating contaminations. On the basis of sequence similarity comparisons to other teleost species and the UniProt databases, functional annotation, and differential expression analysis, we demonstrate the similarity of the transcriptomes among the three species. More than 40% of the transcripts for each species were functionally annotated and about 70% were assigned to orthologous genes of a closely related species. Differential expression analysis between the sexual and unisexual species uncovered 2035 up-regulated and 564 down-regulated genes in P. formosa. This was exemplary validated for six genes by qRT-PCR.
Conclusions
We identified more than 130 genes related to meiosis and reproduction within the apomictically reproducing P. formosa. Overall expression of these genes seems to be down-regulated in the P. formosa transcriptome compared to both ancestral species (i.e., 106 genes down-regulated, 29 up-regulated). A further 35 meiosis and reproduction related genes were not found in the P. formosa transcriptome, but were only expressed in the sexual species. Our data support the hypothesis of general down-regulation of meiosis-related genes in the apomictic Amazon molly. Furthermore, the obtained dataset and identified gene catalog will serve as a resource for future research on the molecular mechanisms behind the reproductive mode of this unisexual species.
Abstract
Background
The unisexual Amazon molly (Poecilia formosa) originated from a hybridization between two sexual species, the sailfin molly (Poecilia latipinna) and the Atlantic molly (Poecilia mexicana). The Amazon molly reproduces clonally via sperm-dependent parthenogenesis (gynogenesis), in which the sperm of closely related species triggers embryogenesis of the apomictic oocytes, but typically does not contribute genetic material to the next generation. We compare for the first time the gonadal transcriptome of the Amazon molly to those of both ancestral species, P. mexicana and P. latipinna.
Results
We sequenced the gonadal transcriptomes of the P. formosa and its parental species P. mexicana and P. latipinna using Illumina RNA-sequencing techniques (paired-end, 100 bp). De novo assembly of about 50 million raw read pairs for each species was performed using Trinity, yielding 106,922 transcripts for P. formosa, 115,175 for P. latipinna, and 133,025 for P. mexicana after eliminating contaminations. On the basis of sequence similarity comparisons to other teleost species and the UniProt databases, functional annotation, and differential expression analysis, we demonstrate the similarity of the transcriptomes among the three species. More than 40% of the transcripts for each species were functionally annotated and about 70% were assigned to orthologous genes of a closely related species. Differential expression analysis between the sexual and unisexual species uncovered 2035 up-regulated and 564 down-regulated genes in P. formosa. This was exemplary validated for six genes by qRT-PCR.
Conclusions
We identified more than 130 genes related to meiosis and reproduction within the apomictically reproducing P. formosa. Overall expression of these genes seems to be down-regulated in the P. formosa transcriptome compared to both ancestral species (i.e., 106 genes down-regulated, 29 up-regulated). A further 35 meiosis and reproduction related genes were not found in the P. formosa transcriptome, but were only expressed in the sexual species. Our data support the hypothesis of general down-regulation of meiosis-related genes in the apomictic Amazon molly. Furthermore, the obtained dataset and identified gene catalog will serve as a resource for future research on the molecular mechanisms behind the reproductive mode of this unisexual species.
Background
The Amazon molly, Poecilia formosa (Teleostei: Poeciliinae) is an unisexual, all-female species. It evolved through the hybridisation of two closely related sexual species and exhibits clonal reproduction by sperm dependent parthenogenesis (or gynogenesis) where the sperm of a parental species is only used to activate embryogenesis of the apomictic, diploid eggs but does not contribute genetic material to the offspring.
Here we provide and describe the first de novo assembled transcriptome of the Amazon molly in comparison with its maternal ancestor, the Atlantic molly Poecilia mexicana. The transcriptome data were produced through sequencing of single end libraries (100 bp) with the Illumina sequencing technique.
Results
83,504,382 reads for the Amazon molly and 81,625,840 for the Atlantic molly were assembled into 127,283 and 78,961 contigs for the Amazon molly and the Atlantic molly, respectively. 63% resp. 57% of the contigs could be annotated with gene ontology terms after sequence similarity comparisons. Furthermore, we were able to identify genes normally involved in reproduction and especially in meiosis also in the transcriptome dataset of the apomictic reproducing Amazon molly.
Conclusions
We assembled and annotated the transcriptome of a non-model organism, the Amazon molly, without a reference genome (de novo). The obtained dataset is a fundamental resource for future research in functional and expression analysis. Also, the presence of 30 meiosis-specific genes within a species where no meiosis is known to take place is remarkable and raises new questions for future research.
Eight polymorphic microsatellite loci were developed for the brook lamprey Lampetra planeri through 454 sequencing and their usefulness was tested in 45 individuals of both L. planeri and the river lamprey Lampetra fluviatilis. The number of alleles per loci ranged between two and five; the Italian and Irish populations had a mean expected heterozygosity of 0.388 and 0.424 and a mean observed heterozygosity of 0.418 and 0.411, respectively. (C) 2014 The Fisheries Society of the British Isles
Objective
We investigated the potential role of indirect benefits for female mate preferences in a highly promiscuous species of live-bearing fishes, the sailfin molly Poecilia latipinna using an integrative approach that combines methods from animal behavior, life-history evolution, and genetics. Males of this species solely contribute sperm for reproduction, and consequently females do not receive any direct benefits. Despite this, females typically show clear mate preferences. It has been suggested that females can increase their reproductive success through indirect benefits from choosing males of higher quality.
Results
Although preferences for large body size have been recorded as an honest signal for genetic quality, this particular study resulted in female preference being unaffected by male body size. Nonetheless, larger males did sire more offspring, but with no effect on offspring quality. This study presents a methodical innovation by combining preference testing with life history measurements—such as the determination of the dry weight of fish embryos—and paternity analyses on single fish embryos.
Objective
We investigated the potential role of indirect benefits for female mate preferences in a highly promiscuous species of live-bearing fishes, the sailfin molly Poecilia latipinna using an integrative approach that combines methods from animal behavior, life-history evolution, and genetics. Males of this species solely contribute sperm for reproduction, and consequently females do not receive any direct benefits. Despite this, females typically show clear mate preferences. It has been suggested that females can increase their reproductive success through indirect benefits from choosing males of higher quality.
Results
Although preferences for large body size have been recorded as an honest signal for genetic quality, this particular study resulted in female preference being unaffected by male body size. Nonetheless, larger males did sire more offspring, but with no effect on offspring quality. This study presents a methodical innovation by combining preference testing with life history measurements—such as the determination of the dry weight of fish embryos—and paternity analyses on single fish embryos.
A recent Science report predicted the global killer whale population to collapse due to PCB pollution. Here we present empirical evidence, which supports and extends the reports’ statement. In 2016, a neonate male killer whale stranded on the German island of Sylt. Neonatal attributes indicated an age of at least 3 days. The stomach contained ∼20 mL milk residue and no pathologies explaining the cause of death could be detected. Blubber samples presenting low lipid concentrations were analysed for persistent organic pollutants. Skin samples were collected for genotyping of the mitochondrial control region. The blubber PCB concentrations were very high [SPCBs, 225 mg/kg lipid weight (lw)], largely exceeding the PCB toxicity thresholds reported for the onset of immunosuppression [9 mg/kg lw ∑PCB] and for severe reproductive impairment [41 mg/kg lw ∑PCB] reported for marine mammals. Additionally, this individual showed equally high concentrations in p,p’-DDE [226 mg/kg lw], PBDEs [5 mg/kg lw] and liver mercury levels [1.1 μg/g dry weight dw]. These results suggest a high placental transfer of pollutants from mother to foetus. Consequently, blubber and plasma PCB concentrations and calf mortality rates are both high in primiparous females. With such high pollutant levels, this neonate had poor prerequisites for survival. The neonate belonged to Ecotype I (generalist feeder) and carried the mitochondrial haplotype 35 present in about 16% of the North Atlantic killer whale from or close to the North Sea. The relevance of this data becomes apparent in the UK West Coast Community, the UK's only residentorca population, which is currently composed of only eight individuals (each four males and females) and no calves have been reported over the last 19 years.Despite worldwide regulations, PCBs persist in the environment and remain a severe concern for killer whale populations, placing calves at high risk due to the mother-offspring PCB-transfer resulting in a high toxicological burden of the neonates.
Investigating the dog genome we found 178965 introns with a moderate length of 200-1000 bp. A screening of these sequences against 23 different repeat libraries to find insertions of short interspersed elements (SINEs) detected 45276 SINEs. Virtually all of these SINEs (98%) belong to the tRNA-derived Can-SINE family. Can-SINEs arose about 55 million years ago before Carnivora split into two basal groups, the Caniformia (doglike carnivores) and the Feliformia (cat-like carnivores). Genome comparisons of dog and cat recovered 506 putatively informative SINE loci for caniformian phylogeny. In this study we show how to use such genome information of model organisms to research the phylogeny of related non-model species of interest. Investigating a dataset including representatives of all major caniformian lineages, we analysed 24 randomly chosen loci for 22 taxa. All loci were amplifiable and revealed 17 parsimony- informative SINE insertions. The screening for informative SINE insertions yields a large amount of sequence information, in particular of introns, which contain reliable phylogenetic information as well. A phylogenetic analysis of intron- and SINE sequence data provided a statistically robust phylogeny which is congruent with the absence/presence pattern of our SINE markers. This phylogeny strongly supports a sistergroup relationship of Musteloidea and Pinnipedia. Within Pinnipedia, we see strong support from bootstrapping and the presence of a SINE insertion for a sistergroup relationship of the walrus with the Otariidae.
The ongoing global amphibian decline calls for an increase of habitat and population management efforts. Pond restoration and construction is more and more accompanied by breeding and translocation programs. However, the appropriateness of translocations as a tool for conservation has been widely debated, as it can cause biodiversity loss through genetic homogenization and can disrupt local adaptation, eventually leading to outbreeding depression. In this study, we investigated the genetic structure of two translocated populations of the critically endangered fire-bellied toad Bombina bombina at its north western distribution edge using supposedly neutral genetic markers (variation in the mitochondrial control region and microsatellites) as well as a marker under selection (major histocompatibility complex (MHC) genes). While one of the newly established populations showed the typical genetic composition of surrounding populations, the other was extremely diverged without clear affinity to its putative source. In this population we detected a profound impact of allochthonous individuals: 100% of the analyzed individuals exhibited a highly divergent mitochondrial haplotype which was otherwise found in Austria. 83% of them were also assigned to Austria by the analysis of microsatellites. Interestingly, for the adaptive marker (MHC) local alleles were predominant in this population, while only very few alleles were shared with the Austrian population. Probably Mendelian inheritance has reshuffled genotypes such that adaptive local alleles are maintained (here, MHC), while presumably neutral allochthonous alleles dominate at other loci. The release of allochthonous individuals generally increased the genetic variability of the affected population without wiping out locally adaptive genotypes. Thus, outbreeding depression might be less apparent than sometimes thought and natural selection appears strong enough to maintain locally adaptive alleles, at least in functionally important immune system genes.
Background
Natural accessions of Arabidopsis thaliana are a well-known system to measure levels of intraspecific genetic variation. Leaf starch content correlates negatively with biomass. Starch is synthesized by the coordinated action of many (iso)enzymes. Quantitatively dominant is the repetitive transfer of glucosyl residues to the non-reducing ends of α-glucans as mediated by starch synthases. In the genome of A. thaliana, there are five classes of starch synthases, designated as soluble starch synthases (SSI, SSII, SSIII, and SSIV) and granule-bound synthase (GBSS). Each class is represented by a single gene. The five genes are homologous in functional domains due to their common origin, but have evolved individual features as well. Here, we analyze the extent of genetic variation in these fundamental protein classes as well as possible functional implications on transcript and protein levels.
Findings
Intraspecific sequence variation of the five starch synthases was determined by sequencing the entire loci including promoter regions from 30 worldwide distributed accessions of A. thaliana. In all genes, a considerable number of nucleotide polymorphisms was observed, both in non-coding and coding regions, and several amino acid substitutions were identified in functional domains. Furthermore, promoters possess numerous polymorphisms in potentially regulatory cis-acting regions. By realtime experiments performed with selected accessions, we demonstrate that DNA sequence divergence correlates with significant differences in transcript levels.
Conclusions
Except for AtSSII, all starch synthase classes clustered into two or three groups of haplotypes, respectively. Significant difference in transcript levels among haplotype clusters in AtSSIV provides evidence for cis-regulation. By contrast, no such correlation was found for AtSSI, AtSSII, AtSSIII, and AtGBSS, suggesting trans-regulation. The expression data presented here point to a regulation by common trans-regulatory transcription factors which ensures a coordinated action of the products of these four genes during starch granule biosynthesis. The apparent cis-regulation of AtSSIV might be related to its role in the initiation of de novo biosynthesis of granules.
Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase; EC 4.1.1.39), the most abundant protein in nature, catalyzes the assimilation of CO(2) (worldwide about 10(11) t each year) by carboxylation of ribulose-1,5-bisphosphate. It is a hexadecamer consisting of eight large and eight small subunits. Although the Rubisco large subunit (rbcL) is encoded by a single gene on the multicopy chloroplast genome, the Rubisco small subunits (rbcS) are encoded by a family of nuclear genes. In Arabidopsis thaliana, the rbcS gene family comprises four members, that is, rbcS-1a, rbcS-1b, rbcS-2b, and rbcS-3b. We sequenced all Rubisco genes in 26 worldwide distributed A. thaliana accessions. In three of these accessions, we detected a gene duplication/loss event, where rbcS-1b was lost and substituted by a duplicate of rbcS-2b (called rbcS-2b*). By screening 74 additional accessions using a specific polymerase chain reaction assay, we detected five additional accessions with this duplication/loss event. In summary, we found the gene duplication/loss in 8 of 100 A. thaliana accessions, namely, Bch, Bu, Bur, Cvi, Fei, Lm, Sha, and Sorbo. We sequenced an about 1-kb promoter region for all Rubisco genes as well. This analysis revealed that the gene duplication/loss event was associated with promoter alterations (two insertions of 450 and 850 bp, one deletion of 730 bp) in rbcS-2b and a promoter deletion (2.3 kb) in rbcS-2b* in all eight affected accessions. The substitution of rbcS-1b by a duplicate of rbcS-2b (i.e., rbcS-2b*) might be caused by gene conversion. All four Rubisco genes evolve under purifying selection, as expected for central genes of the highly conserved photosystem of green plants. We inferred a single positive selected site, a tyrosine to aspartic acid substitution at position 72 in rbcS-1b. Exactly the same substitution compromises carboxylase activity in the cyanobacterium Anacystis nidulans. In A. thaliana, this substitution is associated with an inferred recombination. Functional implications of the substitution remain to be evaluated.
Transitory starch metabolism is a nonlinear and highly regulated process. It originated very early in the evolution of chloroplast-containing cells and is largely based on a mosaic of genes derived from either the eukaryotic host cell or the prokaryotic endosymbiont. Initially located in the cytoplasm, starch metabolism was rewired into plastids in Chloroplastida. Relocation was accompanied by gene duplications that occurred in most starch-related gene families and resulted in subfunctionalization of the respective gene products. Starch-related isozymes were then evolutionary conserved by constraints such as internal starch structure, posttranslational protein import into plastids and interactions with other starch-related proteins. 25 starch-related genes in 26 accessions of Arabidopsis thaliana were sequenced to assess intraspecific diversity, phylogenetic relationships, and modes of selection. Furthermore, sequences derived from additional 80 accessions that are publicly available were analyzed. Diversity varies significantly among the starch-related genes. Starch synthases and phosphorylases exhibit highest nucleotide diversities, while pyrophosphatases and debranching enzymes are most conserved. The gene trees are most compatible with a scenario of extensive recombination, perhaps in a Pleistocene refugium. Most genes are under purifying selection, but disruptive selection was inferred for a few genes/substitutiones. To study transcript levels, leaves were harvested throughout the light period. By quantifying the transcript levels and by analyzing the sequence of the respective accessions, we were able to estimate whether transcript levels are mainly determined by genetic (i.e., accession dependent) or physiological (i.e., time dependent) parameters. We also identified polymorphic sites that putatively affect pattern or the level of transcripts.
Spotlight on islands
(2018)
Groups of proximate continental islands may conceal more tangled phylogeographic patterns than oceanic archipelagos as a consequence of repeated sea level changes, which allow populations to experience gene flow during periods of low sea level stands and isolation by vicariant mechanisms during periods of high sea level stands. Here, we describe for the first time an ancient and diverging lineage of the Italian wall lizard Podarcis siculus from the western Pontine Islands. We used nuclear and mitochondrial DNA sequences of 156 individuals with the aim of unraveling their phylogenetic position, while microsatellite loci were used to test several a priori insular biogeographic models of migration with empirical data. Our results suggest that the western Pontine populations colonized the islands early during their Pliocene volcanic formation, while populations from the eastern Pontine Islands seem to have been introduced recently. The inter-island genetic makeup indicates an important role of historical migration, probably due to glacial land bridges connecting islands followed by a recent vicariant mechanism of isolation. Moreover, the most supported migration model predicted higher gene flow among islands which are geographically arranged in parallel. Considering the threatened status of small insular endemic populations, we suggest this new evolutionarily independent unit be given priority in conservation efforts.
Spotlight on islands
(2018)
Groups of proximate continental islands may conceal more tangled phylogeographic patterns than oceanic archipelagos as a consequence of repeated sea level changes, which allow populations to experience gene flow during periods of low sea level stands and isolation by vicariant mechanisms during periods of high sea level stands. Here, we describe for the first time an ancient and diverging lineage of the Italian wall lizard Podarcis siculus from the western Pontine Islands. We used nuclear and mitochondrial DNA sequences of 156 individuals with the aim of unraveling their phylogenetic position, while microsatellite loci were used to test several a priori insular biogeographic models of migration with empirical data. Our results suggest that the western Pontine populations colonized the islands early during their Pliocene volcanic formation, while populations from the eastern Pontine Islands seem to have been introduced recently. The inter-island genetic makeup indicates an important role of historical migration, probably due to glacial land bridges connecting islands followed by a recent vicariant mechanism of isolation. Moreover, the most supported migration model predicted higher gene flow among islands which are geographically arranged in parallel. Considering the threatened status of small insular endemic populations, we suggest this new evolutionarily independent unit be given priority in conservation efforts.
We analyzed mtDNA polymorphisms (a total of 741 bp from a part of conserved control region, ND5, ND2, Cyt b and 12S) in 91 scats and 12 tissue samples of Bengal tiger (Panthera tigris tigris) populations across Terai Arc Landscape (TAL) located at the foothills of Himalayas in North Western India, Buxa Tiger Reserve (BTR), and North East India. In TAL and BTR, we found a specific haplotype at high frequency, which was absent elsewhere, indicating a genetically distinct population in these regions. Within the TAL region, there is some evidence for genetic isolation of the tiger populations west of river Ganges, i.e., in the western part of Rajaji National Park (RNP). Although the river itself might not constitute a significant barrier for tigers, recent human-induced changes in habitat and degradation of the Motichur-Chilla Corridor connecting the two sides of the tiger habitat of RNP might effectively prevent genetic exchange. A cohesive population is observed for the rest of the TAL. Even the more eastern BTR belongs genetically to this unit, despite the present lack of a migration corridor between BTR and TAL. In spite of a close geographic proximity, Chitwan (Nepal) constitutes a tiger population genetically different from TAL. Moreover, it is observed that the North East India tiger populations are genetically different from TAL and BTR, as well as from the other Bengal tiger populations in India.
We analyzed mtDNA polymorphisms (parts of control region, ND5, ND2, Cytb, 12S, together 902 bp) in 59 scat and 18 tissue samples from 13 Indian populations of the critically endangered Indian tiger (Panthera tigris tigris), along with zoo animals as reference. Northern tiger populations exhibit two unique haplotypes suggesting genetic isolation. Western populations from Sariska (extinct in 2004) and Ranthambore are genetically similar, such that Ranthambore could serve as a source for reintroduction in Sariska. Zoo populations maintain mitochondrial lineages that are rare or absent in the wild.