Thyroid hormone divergence between two closely related but ecologically diverse cyprinid fish species (Cyprinidae)

Thyroid hormones (THs) are involved in regulation of many life history traits of fishes. Development, growth, reproduction and shaping the adult phenotypes were found to be regulated by THs. Regulatory evolution is one of the main factors driving morpho-ecological diversification and speciation. We tested a hypothesis whether closely related but ecologically diverged species may have a diverse level of THs. We compared seasonal levels of plasma concentrations of triiodothyronine (T₃) in two cyprinid species, benthophagous bream Abramis brama and zooplanktivorous blue bream Ballerus ballerus. Significant differences in T₃ concentrations were detected. B. ballerus had substantially reduced T₃ levels as compared to most other species of fish. Two hypotheses explaining the thyroid divergence are discussed. Despite differences in absolute T₃ concentrations, both species manifest similar seasonal cycling with increased plasma T₃ levels in warmer seasons and decreased T₃ in colder seasons. Several peaks of plasma T₃ level were registered: at pre-spawning periods, at mid-summer and in the early autumn. The pre-spawning peak noted in cyprinids was a novel observation. Significant positive correlations were detected between water temperature and plasma T₃ concentrations, as well as between the duration of daylight and T₃ plasma concentrations in both species.     

Climatic adaptation and ecological divergence between two closely related pine species in Southeast China

Climate is one of the most important drivers for adaptive evolution in forest trees. Climatic selection contributes greatly to local adaptation and intraspecific differentiation, but this kind of selection could also have promoted interspecific divergence through ecological speciation. To test this hypothesis, we examined intra‐ and interspecific genetic variation at 25 climate‐related candidate genes and 12 reference loci in two closely related pine species, Pinus massoniana Lamb. and Pinus hwangshanensis Hisa, using population genetic and landscape genetic approaches. These two species occur in Southeast China but have contrasting ecological preferences in terms of several environmental variables, notably altitude, although hybrids form where their distributions overlap. One or more robust tests detected signals of recent and/or ancient selection at two‐thirds (17) of the 25 candidate genes, at varying evolutionary timescales, but only three of the 12 reference loci. The signals of recent selection were species specific, but signals of ancient selection were mostly shared by the two species likely because of the shared evolutionary history. F_ST outlier analysis identified six SNPs in five climate‐related candidate genes under divergent selection between the two species. In addition, a total of 24 candidate SNPs representing nine candidate genes showed significant correlation with altitudinal divergence in the two species based on the covariance matrix of population history derived from reference SNPs. Genetic differentiation between these two species was higher at the candidate genes than at the reference loci. Moreover, analysis using the isolation‐with‐migration model indicated that gene flow between the species has been more restricted for climate‐related candidate genes than the reference loci, in both directions. Taken together, our results suggest that species‐specific and divergent climatic selection at the candidate genes might have counteracted interspecific gene flow and played a key role in the ecological divergence of these two closely related pine species.     

Host specialization by reproductive interference between closely related herbivorous insects

Host specialization among closely related herbivores is common and is therefore a major theme in ecology. Despite its ecological importance, no general explanatory framework for host specialization is currently available. We introduce a new model of the evolution of host specialization in herbivorous insects. We use a two-dimensional lattice comprising 32 × 32 cells. Moreover, the model incorporates reproductive interference, defined as any negative outcomes resulting from interspecific mating, between two species of herbivores feeding on two different host plants as well as ordinary resource competition and differences in host suitability. Our simulation showed that reproductive interference, together with other factors such as host-related performance and resource competition, can actually drive the evolution of host specialization and thereby host partitioning between herbivorous insects during secondary contact. Host specialization arises particularly when levels of both reproductive interference and resource competition are intermediate. In contrast, host specialization seldom occurs if reproductive interference is absent. Thus, reproductive interference is as key to specialization as is spatial partitioning, which was not regarded as a realistic outcome when only resource competition was considered.     

Habitat or prey specialization in predatory ladybird beetles: a case study of two closely related species

This study examines the niche and diet breadth of two closely related sympatric aphidophagous ladybirds: Adalia decempunctata and A. bipunctata. The degree of habitat specialization of these species is investigated, and its effect on life history traits of females is explored. The importance of prey quality in determining the diet breadth is also examined. The niches occupied by these species in three countries, the UK, Belgium and southern France, are similar: A. decempunctata is an arboreal habitat specialist with a narrower set of prey than A. bipunctata, which is commonly found on several types of vegetation. The niches of the two species overlap on trees. Experiments indicate that habitat specialization has resulted in A. decempunctata investing more in each of its offspring than A. bipunctata. A. decempunctata females lay, relative to their body size, heavier eggs than those of the more generalist A. bipunctata, which results in A. decempunctata having bigger larvae. In addition, A. decempunctata larvae are better at surviving starvation than A. bipunctata larvae. In contrast to the expected pattern in food specialization, our study failed to demonstrate a better efficiency of the specialist when fed its usual prey and a detrimental effect when fed on prey that it is unlikely to encounter in the field. The reproductive performance of the specialist ladybird was better when fed an aphid that it was unlikely to regularly feed on in the field. Therefore, the narrow diet of the specialist ladybird is most likely a consequence of it occupying a narrow habitat rather than the quality of the prey. Although further studies on specialization in predatory insects are needed, the results indicate that unlike the role of plant quality in host specialization in herbivorous insects, prey quality has not been the main determinant of ecological specialization in these predatory insects.     

Recombination rate variation in closely related species

Despite their importance to successful meiosis and various evolutionary processes, meiotic recombination rates sometimes vary within species or between closely related species. For example, humans and chimpanzees share virtually no recombination hotspot locations in the surveyed portion of the genomes. However, conservation of recombination rates between closely related species has also been documented, raising an apparent contradiction. Here, we evaluate how and why conflicting patterns of recombination rate conservation and divergence may be observed, with particular emphasis on features that affect recombination, and the scale and method with which recombination is surveyed. Additionally, we review recent studies identifying features influencing fine-scale and broad-scale recombination patterns and informing how quickly recombination rates evolve, how changes in recombination impact selection and evolution in natural populations, and more broadly, which forces influence genome evolution.     

The joint allele-frequency spectrum in closely related species

We develop the theory for computing the joint frequency spectra of alleles in two closely related species. We allow for arbitrary population growth in both species after they had a common ancestor. We focus on the case in which a single chromosome is sequenced from one of the species. We use classical diffusion theory to show that, if the ancestral species was at equilibrium under mutation and drift and a chromosome from one of the descendant species carries the derived allele, the frequency spectrum in the other species is uniform, independently of the demographic history of both species. We also predict the expected densities of segregating and fixed sites when the chromosome from the other species carries the ancestral allele. We compare the predictions of our model with the site-frequency spectra of SNPs in the four HapMap populations of humans when the nucleotide present in the Neanderthal DNA sequence is ancestral or derived, using the chimp genome as the outgroup.     

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.     

Effects of body size on sex‐related migration vary between two closely related gull species with similar size dimorphism

Studies of migration have revealed multiple trade‐offs with other life‐history traits that may underlie observed variation in migratory properties among ages and sexes. To assess whether, and to what extent, body size and/or sex‐specific differences in competition for resources (e.g. breeding territories or winter food) may shape variation in migration distance and timing of arrival in ecologically and phylogenetically related species, we combined over 30 000 sightings of individually marked, sexually mature males and females of Herring Gulls Larus argentatus and Lesser Black‐Backed Gulls Larus fuscus with biometric measurements and phenological observations at a mixed breeding colony. In L. argentatus, larger males migrated further from the breeding colony, whereas migration distance was independent of body size in adult females. In L. fuscus, no relationship between body size and migration distance was apparent in either sex. Mean arrival dates at the breeding colony did not vary with migration distances but differed between males and females of L. argentatus (but not L. fuscus). As allometry at least partly explains sexual segregation in migration behaviour in L. argentatus, but not in L. fuscus, we conclude that the effect of body size on sex‐related migratory strategies may vary between closely related, sympatric species despite similar size dimorphism.     

Exploring species limits in two closely related Chinese oaks

BACKGROUND: The species status of two closely related Chinese oaks, Quercus liaotungensis and Q. mongolica, has been called into question. The objective of this study was to investigate the species status and to estimate the degree of introgression between the two taxa using different approaches. METHODOLOGY/PRINCIPAL FINDINGS: Using SSR (simple sequence repeat) and AFLP (amplified fragment length polymorphism) markers, we found that interspecific genetic differentiation is significant and higher than the differentiation among populations within taxa. Bayesian clusters, principal coordinate analysis and population genetic distance trees all classified the oaks into two main groups consistent with the morphological differentiation of the two taxa rather than with geographic locations using both types of markers. Nevertheless, a few individuals in Northeast China and many individuals in North China have hybrid ancestry according to Bayesian assignment. One SSR locus and five AFLPs are significant outliers against neutral expectations in the interspecific FST simulation analysis, suggesting a role for divergent selection in differentiating species. MAIN CONCLUSIONS/SIGNIFICANCE: All results based on SSRS and AFLPS reached the same conclusion: Q. liaotungensis and Q. mongolica maintain distinct gene pools in most areas of sympatry. They should therefore be considered as discrete taxonomic units. Yet, the degree of introgression varies between the two species in different contact zones, which might be caused by different population history or by local environmental factors.     

Complex genetic patterns in closely related colonizing invasive species

Anthropogenic activities frequently result in both rapidly changing environments and translocation of species from their native ranges (i.e., biological invasions). Empirical studies suggest that many factors associated with these changes can lead to complex genetic patterns, particularly among invasive populations. However, genetic complexities and factors responsible for them remain uncharacterized in many cases. Here, we explore these issues in the vase tunicate Ciona intestinalis (Ascidiacea: Enterogona: Cionidae), a model species complex, of which spA and spB are rapidly spreading worldwide. We intensively sampled 26 sites (N = 873) from both coasts of North America, and performed phylogenetic and population genetics analyses based on one mitochondrial fragment (cytochrome c oxidase subunit 3-NADH dehydrogenase subunit I, COX3-ND1) and eight nuclear microsatellites. Our analyses revealed extremely complex genetic patterns in both species on both coasts. We detected a contrasting pattern based on the mitochondrial marker: two major genetic groups in C. intestinalis spA on the west coast versus no significant geographic structure in C. intestinalis spB on the east coast. For both species, geo-graphically distant populations often showed high microsatellite-based genetic affinities whereas neighboring ones often did not. In addition, mitochondrial and nuclear markers provided largely inconsistent genetic patterns. Multiple factors, including random genetic drift associated with demographic changes, rapid selection due to strong local adaptation, and varying propensity for human-mediated propagule dispersal could be responsible for the observed genetic complexities.     

Inversions in evolution of man and closely related species

By the comparative study of the karyotypes of many Primates, 35 inversions (25 peri- and 10 paracentric) having accumulated during evolution of species related to man were reconstructed. Some of them originated human chromosomes from more ancestral chromosomes still present in other primate species. Their detection in man would indicate the occurrence of reverse mutations. Other inversions occurred in ancestral chromosomes identical to those of man, and originated chromosomes of other Primates species. Their detection in man would indicate the occurrence of a convergent mutation. It is shown that such reverse and convergent mutations do occur. They are too frequently observed than by mere chance among patients ascertained in human cytogenetic laboratories. Their excess is still larger among radiation induced inversions in human cells. This demonstrates the nonrandom occurrence of inversions. In addition, it is concluded that inversions which have accumulated during evolution are more representative of mutagenesis than those detected in human cytogenetic laboratories.     

Retrotranspositions in orthologous regions of closely related grass species

Background  

Retrotransposons are commonly occurring eukaryotic transposable elements (TEs). Among these, long terminal repeat (LTR) retrotransposons are the most abundant TEs and can comprise 50–90% of the genome in higher plants. By comparing the orthologous chromosomal regions of closely related species, the effects of TEs on the evolution of plant genomes can be studied in detail.     

Upper thermal tolerance of closely related Danio species

The main finding of this study was that measuring maximum heart rate during incremental warming was an effective tool to estimate upper thermal limits in three small cyprinid Danio species, which differed significantly. Arrhenius breakpoint temperature for maximum heart rate, purportedly an index of optimum temperature, was 21·2 ± 0·4, 20·1 ± 0·4 and 18·9 ± 0·8° C (mean ± s.e .) for zebrafish Danio rerio, pearl danio Danio albolineatus and glowlight danio Danio choprae, respectively. The temperature where cardiac arrhythmias were first induced during warming (T_arr) was 36·6 ± 0·7, 36·9 ± 0·8 and 33·2 ± 0·8° C (mean ± s.e .) and critical thermal maximum (T_Cm) was 39·9 ± 0·1, 38·9 ± 0·1 and 37·2 ± 0·1° C (mean ± s.e .) for D. rerio, D. albolineatus and D. choprae, respectively. The finding that T_arr was consistently 3–4° C lower than T_Cm suggests that collapse of the cardiac life support system may be a critical trigger for upper temperature tolerance. The upper thermal limits established here, which correlate well with a broad natural environmental temperature range for D. rerio and a narrow one for D. choprae, suggest that upper thermal tolerance may be a genetic trait even among closely related species acclimated to common temperatures.     

Long-term and fine-scale coexistence of closely related species

Models of coexistence often assume that competitive exclusion takes place at fine scale, but that disturbances (non-equilibrium models) or heterogeneity (spatial models) are necessary for long-term coexistence. As an alternative, very slow exclusion among competitively equivalent species has been proposed, but questioned on the ground that in the long run even the smallest difference in competitive ability will express itself in the loss of species. In this paper we demonstrate long-term coexistence among closely-related mire plant species (notablySphagnum mosses). In any bog in the boreal region, most species that can tolerate the nutrient-poor, acidic and partly anaerobic conditions are present. Thus, the ratio between the actual and regional species pool is 1 (or very close to 1), and selection of species from the regional pool seems hardly affected by interspecific competition or dispersal limitation.     

Distinct male reproductive strategies in two closely related oak species

Reproductive strategies of closely related species distributed along successional gradients should differ as a consequence of the trade‐off between competition and colonization abilities. We compared male reproductive strategies of Quercus robur and Q. petraea, two partly interfertile European oak species with different successional status. In the studied even‐aged stand, trees of the late‐successional species (Q. petraea) grew faster and suffered less from intertree competition than trees of the early‐successional species (Q. robur). A large‐scale paternity study and a spatially explicit individual‐based mating model were used to estimate parameters of pollen production and dispersal as well as sexual barriers between species. Male fecundity was found to be dependent both on a tree's circumference and on its environment, particularly so for Q. petraea. Pollen dispersal was greater and more isotropic in Q. robur than in Q. petraea. Premating barriers to hybridization were strong in both species, but more so in Q. petraea than in Q. robur. Hence, predictions based on the competition–colonization trade‐off are well supported, whereas the sexual barriers themselves seem to be shaped by colonization dynamics.     

Competitive strategies differentiate closely related species of marine actinobacteria

Although competition, niche partitioning, and spatial isolation have been used to describe the ecology and evolution of macro-organisms, it is less clear to what extent these principles account for the extraordinary levels of bacterial diversity observed in nature. Ecological interactions among bacteria are particularly challenging to address due to methodological limitations and uncertainties over how to recognize fundamental units of diversity and link them to the functional traits and evolutionary processes that led to their divergence. Here we show that two closely related marine actinomycete species can be differentiated based on competitive strategies. Using a direct challenge assay to investigate inhibitory interactions with members of the bacterial community, we observed a temporal difference in the onset of inhibition. The majority of inhibitory activity exhibited by Salinispora arenicola occurred early in its growth cycle and was linked to antibiotic production. In contrast, most inhibition by Salinispora tropica occurred later in the growth cycle and was more commonly linked to nutrient depletion or other sources. Comparative genomics support these differences, with S. arenicola containing nearly twice the number of secondary metabolite biosynthetic gene clusters as S. tropica, indicating a greater potential for secondary metabolite production. In contrast, S. tropica is enriched in gene clusters associated with the acquisition of growth-limiting nutrients such as iron. Coupled with differences in growth rates, the results reveal that S. arenicola uses interference competition at the expense of growth, whereas S. tropica preferentially employs a strategy of exploitation competition. The results support the ecological divergence of two co-occurring and closely related species of marine bacteria by providing evidence they have evolved fundamentally different strategies to compete in marine sediments.