Habitat-dependent song divergence at subspecies level in the grey-breasted wood-wren

Song divergence among populations can theoretically lead to reproductive divergence and speciation. Despite many studies, this theory is still controversial. Habitat differences have been shown to shape songs, but few studies have looked for a link between ecologically driven acoustic and genetic divergence. We tested whether environmental selection has driven song divergence in two genetically distinct, but hybridizing, subspecies of the grey-breasted wood-wren (Henicorhina leucophrys) in Ecuador. Several acoustic features showed significant divergence between the subspecies. Spectral song divergence correlated with ambient noise profiles which differed significantly between the habitats of both subspecies. Temporal song divergence also corresponded as expected to vegetation density. However, in terms of quantified levels of reverberations, we found no significant differences in habitat-dependent sound transmission properties. We conclude that ecological niche segregation may explain acoustic divergence among the two wren subspecies. The resulting habitat-dependent song divergence may have contributed to reproductive divergence by guiding assortative mating in parapatric conditions or just currently contribute to maintenance of reproductive isolation upon secondary contact.     

Influence of gene flow on divergence dating – implications for the speciation history of Takydromus grass lizards

Dating the time of divergence and understanding speciation processes are central to the study of the evolutionary history of organisms but are notoriously difficult. The difficulty is largely rooted in variations in the ancestral population size or in the genealogy variation across loci. To depict the speciation processes and divergence histories of three monophyletic Takydromus species endemic to Taiwan, we sequenced 20 nuclear loci and combined with one mitochondrial locus published in GenBank. They were analysed by a multispecies coalescent approach within a Bayesian framework. Divergence dating based on the gene tree approach showed high variation among loci, and the divergence was estimated at an earlier date than when derived by the species‐tree approach. To test whether variations in the ancestral population size accounted for the majority of this variation, we conducted computer inferences using isolation‐with‐migration (IM) and approximate Bayesian computation (ABC) frameworks. The results revealed that gene flow during the early stage of speciation was strongly favoured over the isolation model, and the initiation of the speciation process was far earlier than the dates estimated by gene‐ and species‐based divergence dating. Due to their limited dispersal ability, it is suggested that geographical isolation may have played a major role in the divergence of these Takydromus species. Nevertheless, this study reveals a more complex situation and demonstrates that gene flow during the speciation process cannot be overlooked and may have a great impact on divergence dating. By using multilocus data and incorporating Bayesian coalescence approaches, we provide a more biologically realistic framework for delineating the divergence history of Takydromus.     

The origin of ecological divergence in Helianthus paradoxus (Asteraceae): selection on transgressive characters in a novel hybrid habitat

Diploid hybrid speciation in plants is often accompanied by rapid ecological divergence between incipient neospecies and their parental taxa. One plausible means by which novel adaptation in hybrid lineages may arise is transgressive segregation, that is, the generation of extreme phenotypes that exceed those of the parental lines. Early generation (BC2) hybrids between two wild, annual sunflowers, Helianthus annuus and Helianthus petiolaris, were used to study directional selection on transgressive characters associated with the origin of Helianthus paradoxus, a diploid hybrid species adapted to extremely saline marshes. The BC2 plants descended from a single F1 hybrid backcrossed toward H. petiolaris. The strength of selection on candidate adaptive traits in the interspecific BC2 was measured in natural H. paradoxus salt marsh habitat. Positive directional selection was detected for leaf succulence and Ca uptake, two traits that are known to be important in salt stress response in plants. Strong negative directional selection operated on uptake of Na and correlated elements. A significant decrease in trait correlations over time was observed in the BC2 population for Na and Ca content, suggesting an adaptive role for increased Ca uptake coupled with increased net exclusion of Na from leaves. Patterns of directional selection in BC2 hybrids were concordant with character expression in the natural hybrid species, H. paradoxus, transplanted into the wild. Moreover, the necessary variation for generating the H. paradoxus phenotype existed only in the BC2 population, but not in samples of the two parental species, H. annuus and H. petiolaris. These results are consistent with the hypothesis that transgressive segregation of elemental uptake and leaf succulence contributed to the origin of salt adaptation in the diploid hybrid species H. paradoxus.     

Genomics of the divergence continuum in an African plant biodiversity hotspot,I: drivers of population divergence in Restio capensis (Restionaceae)

Understanding the drivers of population divergence, speciation and species persistence is of great interest to molecular ecology, especially for species‐rich radiations inhabiting the world's biodiversity hotspots. The toolbox of population genomics holds great promise for addressing these key issues, especially if genomic data are analysed within a spatially and ecologically explicit context. We have studied the earliest stages of the divergence continuum in the Restionaceae, a species‐rich and ecologically important plant family of the Cape Floristic Region (CFR) of South Africa, using the widespread CFR endemic Restio capensis (L.) H.P. Linder & C.R. Hardy as an example. We studied diverging populations of this morphotaxon for plastid DNA sequences and >14 400 nuclear DNA polymorphisms from Restriction site Associated DNA (RAD) sequencing and analysed the results jointly with spatial, climatic and phytogeographic data, using a Bayesian generalized linear mixed modelling (GLMM) approach. The results indicate that population divergence across the extreme environmental mosaic of the CFR is mostly driven by isolation by environment (IBE) rather than isolation by distance (IBD) for both neutral and non‐neutral markers, consistent with genome hitchhiking or coupling effects during early stages of divergence. Mixed modelling of plastid DNA and single divergent outlier loci from a Bayesian genome scan confirmed the predominant role of climate and pointed to additional drivers of divergence, such as drift and ecological agents of selection captured by phytogeographic zones. Our study demonstrates the usefulness of population genomics for disentangling the effects of IBD and IBE along the divergence continuum often found in species radiations across heterogeneous ecological landscapes.     

The acoustic ecology of an Amazonian bird assemblage: the role of allometry,competition and environmental filtering in the acoustic structure

Communication among birds constitutes the foundation of social interactions, and acoustic signals should evolve based on their efficiency to convey information. We examined the acoustic signals of an Amazonian bird assemblage by testing whether vocal allometry was the main driver in song evolution. We expected the acoustic parameters of the songs to follow general allometric rules, as the size of the vocal apparatus limits the vibration capacity of the syrinx. We tested whether smaller species use lower than expected frequencies due to environmental filtering by examining deviations from allometric relationships. Alternatively, small species could use higher than expected frequencies as a consequence of competitive processes that promote the use of vacant portions of the acoustic spectrum. We recorded birdsongs between 2013 and 2018 and measured three spectral parameters: the dominant frequency (FDOM), the minimum fundamental frequency (FFMIN) and the maximum fundamental frequency (FFMAX). We created an allometric model based on the acoustic pattern of the larger species and used it to predict the frequencies of the smaller species. We compared the frequency values expected by allometry with the observed parameters of the avian assemblage. We found that FDOM and FFMIN were higher than expected by allometry alone, supporting competition structuring in the acoustic ecology of the assemblage. The successful insertion of many species into the acoustic space is the result of long processes of natural selection, with our data highlighting the importance of competition in the vocal structuring of the community.     

Natural selection on a vertical environmental gradient in Littorina saxatilis: analysis of fecundity

Two different morphs of the intertidal snail Littorina saxatilis are found in the wave-exposed coasts of Galicia, NW Spain. One lives on the upper shore and the other on the lower shore. They meet and produce phenotypically intermediate hybrids in a narrow transition band on the mid-shore. To understand the maintenance in sympatry of such an extreme intraspecific polymorphism, we studied the change in fecundity in each morph along two vertical transects of the coast. We did not find a progressive reduction in fecundity in any morph as it approached the midshore, and conclude therefore that the observed spatial segregation of the morphs cannot be explained by divergent natural selection acting through fecundity. We also measured 16 environmental variables, but none explained an important proportion of fecundity variability.     

Geographical variation in acoustic signals of the planthopper, Nilaparvata bakeri (Muir), in Asia: species recognition and sexual selection

Populations of the planthopper .Nilaparvata bakeri (Muir) were sampled from the Philippines (Luzon), Indonesia (Bali), India (Bihar) and Sri Lanka (Central Province) from the grass Leersia hexandra (Schwartz), and cultured in Cardiff. Low intensity vibratory signals produced by males and females during mate location and courtship were recorded and analysed. Obvious differences were found between male calling songs of insects from the Philippines and those from the other three areas. Smaller differences were detected between the Indonesian, Indian and Sri Lankan populations. Hybrids between Philippine and Indonesian, and Indonesian and Sri Lankan, insects were obtained freely in the laboratory. Male calls of F, hybrids were variable and intermediate between parentals. Mate choice experiments showed no significant assortative mating between the different populations. There was no indication of reproductive isolation and therefore of different biological species. The assumption that different male calling songs necessarily indicate the presence of different biological species is not confirmed in this example.     

A test of the Acoustic Adaptation Hypothesis in three types of tropical forest: degradation of male and female Rufous-and-white Wren songs

Many animals produce complex vocalizations that show pronounced variation between populations. The Acoustic Adaptation Hypothesis helps to explain this variation, suggesting that acoustic signals are optimized for transmission through different environments. Little is known about the transmission properties of female vocalizations because most studies of the Acoustic Adaptation Hypothesis have focused on male vocalizations of organisms living at temperate latitudes. We explored the relationship between environmental variation and the transmission properties of songs of Rufous-and-white Wrens, resident Neotropical songbirds where both sexes sing. Using playback, we broadcast and re-recorded elements of male and female songs from three populations of wrens living in three different forest habitats in Costa Rica. We measured four variables of the re-recorded sounds: signal-to-noise ratio, excess attenuation, tail-to-signal ratio and blur ratio. Our results show a significant difference between transmission characteristics of both male and female song elements across the three habitats, indicating that sounds transmit differently through different types of tropical forest. The population from which the broadcast sounds were recorded (source population) had little effect on sound transmission, however, suggesting that acoustic differences between these populations may not arise through acoustic adaptation to these habitats. Male and female elements showed similar transmission properties overall, although signal-to-noise ratio of male elements was influenced by source population, whereas blur ratio and excess attenuation of female elements were influenced by source population. Our study highlights the differences in transmission characteristics of animal sounds through different habitats, and reveals some sex differences in transmission properties.     

Divergent natural selection with gene flow along major environmental gradients in Amazonia: insights from genome scans, population genetics and phylogeography of the characin fish Triportheus albus

The unparalleled diversity of tropical ecosystems like the Amazon Basin has been traditionally explained using spatial models within the context of climatic and geological history. Yet, it is adaptive genetic diversity that defines how species evolve and interact within an ecosystem. Here, we combine genome scans, population genetics and sequence-based phylogeographic analyses to examine spatial and ecological arrangements of selected and neutrally evolving regions of the genome of an Amazonian fish, Triportheus albus. Using a sampling design encompassing five major Amazonian rivers, three hydrochemical settings, 352 nuclear markers and two mitochondrial DNA genes, we assess the influence of environmental gradients as biodiversity drivers in Amazonia. We identify strong divergent natural selection with gene flow and isolation by environment across craton (black and clear colour)- and Andean (white colour)-derived water types. Furthermore, we find that heightened selection and population genetic structure present at the interface of these water types appears more powerful in generating diversity than the spatial arrangement of river systems and vicariant biogeographic history. The results from our study challenge assumptions about the origin and distribution of adaptive and neutral genetic diversity in tropical ecosystems. In addition, they have important implications for measures of biodiversity and evolutionary potential in one of the world's most diverse and iconic ecosystems.     

Adaptive divergence and the evolution of reproductive isolation in the wild: an empirical demonstration using introduced sockeye salmon

Populations exposed to different ecological environments should diverge for phenotypic traits that influence survival and reproduction. This adaptive divergence should reduce gene flow between populations because immigrants become less fit than residents and because hybrids perform poorly in either environment (i.e., ecologically-dependent reproductive isolation). Here I demonstrate adaptive divergence and the evolution of reproductive isolation in populations of sockeye salmon (Oncorhynchus nerka) introduced from a common ancestral source into a new lake system (Lake Washington, Washington). The introduced fish founded several new populations, two of which experience very different environments during breeding and early development (Cedar River v.s. Pleasure Point beach). Over 13 generations, the two populations diverged for adult traits (female body size, male body depth; measured in the wild) and embryo traits (survival to hatching, development rate, size at emergence; measured in a common environment). The rates of divergence for these characters were similar to those observed in other examples of rapid evolution, and can best be attributed to natural selection. Partial reproductive isolation has evolved in concert with adaptive divergence: the rate of exchange of adults between the populations (determined using natural tags) is higher than the rate of gene flow (determined using DNA microsatellites). The demonstration that adaptive divergence can initiate reproductive isolation in less than 13 generations suggests that the first signs of ecological speciation may appear soon after new environments are first colonized.     

Geographical and seasonal variation in the intensity of sexual selection in the barn swallow Hirundo rustica: a meta‐analysis

Sexual selection arises from competition among individuals for access to mates, resulting in the evolution of conspicuous sexually selected traits, especially when inter‐sexual competition is mediated by mate choice. Different sexual selection regimes may occur among populations/subspecies within the same species. This is particularly the case when mate choice is based on multiple sexually selected traits. However, empirical evidence supporting this hypothesis at the among‐populations level is scarce. We conducted a meta‐analysis of the intensity of sexual selection on the largest database to date for a single species, the barn swallow (Hirundo rustica), relying on quantitative estimates of sexual selection. The intensity of sexual selection was expressed as the strength (effect size) of the relationships between six plumage ornaments (tail length, tail asymmetry, size of white spots on tail, ventral plumage colour, throat plumage colour and throat patch size) and several fitness proxies related to reproduction, parental care, offspring quality, arrival date from spring migration, and survival. The data were gathered for four geographically separated subspecies (H. r. rustica, H. r. erythrogaster, H. r. gutturalis, H. r. transitiva). The overall mean effect size (Z_r = 0.214; 95% confidence interval = 0.175–0.254; N = 329) was of intermediate magnitude, with intensity of sexual selection being stronger in males than in females. Effect sizes varied during the breeding cycle, being larger before egg deposition, when competition for access to mates reaches its maximum (i.e. in the promiscuous part of the breeding cycle), and decreasing thereafter. In addition, effect sizes from experiments were not significantly larger than those from correlative studies. Finally, sexual selection on different sexually dimorphic traits varied among subspecies. This last result suggests that morphological divergence among populations has partly arisen from divergent sexual selection, which may eventually lead to speciation.     

Phylogenetic and phylogeographic analysis of the genus Orestias (Teleostei: Cyprinodontidae) in the southern Chilean Altiplano: the relevance of ancient and recent divergence processes in speciation

This study presents phylogenetic molecular data of the Chilean species of Orestias to propose an allopatric divergence hypothesis and phylogeographic evidence that suggests the relevance of abiotic factors in promoting population divergence in this complex. The results reveal that diversification is still ongoing, e.g. in the Ascotán salt pan, where populations of Orestias ascotanensis restricted to individual freshwater springs exhibit strong genetic differentiation, reflecting putative independent evolutionary units. Diversification of Orestias in the southern Altiplano may be linked to historical vicariant events and contemporary variation in water level; these processes may have affected the populations from the Plio‐Pleistocene until the present.     

The tempo of trait divergence in geographic isolation: Avian speciation across the Marañon Valley of Peru

Geographic isolation is considered essential to most speciation events, but our understanding of what controls the pace and degree of phenotypic divergence among allopatric populations remains poor. Why do some taxa exhibit phenotypic differentiation across barriers to dispersal, whereas others do not? To test factors controlling phenotypic divergence in allopatry, we employed a comparative phylogeographic approach consisting of replicates of ecologically similar Andean bird species isolated across a major biogeographic barrier, the Marañon Valley of Peru. Our study design leverages variation among codistributed taxa in their degree of plumage, morphometric, and vocal differentiation across the Marañon to examine the tempo of phenotypic evolution. We found that substantial plumage differences between populations required roughly two million years to evolve. In contrast, morphometric trait evolution showed greater idiosyncrasy and stasis. Our results demonstrate that despite a large degree of idiosyncrasy in the relationship between genetic and phenotypic divergence across taxa and environments, comparative studies within regions may reveal predictability in the pace of phenotypic divergence. Our results also suggest that social selection is important for driving differentiation of populations found in similar environments.     

Context dependence in complex adaptive landscapes: frequency and trait‐dependent selection surfaces within an adaptive radiation of Caribbean pupfishes

The adaptive landscape provides the foundational bridge between micro‐ and macroevolution. One well‐known caveat to this perspective is that fitness surfaces depend on ecological context, including competitor frequency, traits measured, and resource abundance. However, this view is based largely on intraspecific studies. It is still unknown how context‐dependence affects the larger features of peaks and valleys on the landscape which ultimately drive speciation and adaptive radiation. Here, I explore this question using one of the most complex fitness landscapes measured in the wild in a sympatric pupfish radiation endemic to San Salvador Island, Bahamas by tracking survival and growth of laboratory‐reared F2 hybrids. I present new analyses of the effects of competitor frequency, dietary isotopes, and trait subsets on this fitness landscape. Contrary to expectations, decreasing competitor frequency increased survival only among very common phenotypes, whereas less common phenotypes rarely survived despite few competitors, suggesting that performance, not competitor frequency, shapes large‐scale features of the fitness landscape. Dietary isotopes were weakly correlated with phenotype and growth, but did not explain additional survival variation. Nonlinear fitness surfaces varied substantially among trait subsets, revealing one‐, two‐, and three‐peak landscapes, demonstrating the complexity of selection in the wild, even among similar functional traits.     

A spatial analysis of the ecology and morphology of cicadas in the Pauropsalta annulata species complex (Hemiptera: Cicadidae)

The cicada Pauropsalta annulata Goding & Froggatt, 1904 comprises several distinct song types across its known distribution in eastern Australia, with these songs being statistically distinguishable from one another. Here we use spatial analysis of adult morphology and plant species associations to test further the hypothesis that P. annulata song types represent a complex of cryptic species. To structure this investigation we contrast different approaches and expectations given under the framework of ecological speciation with those of the recognition concept of species. Plotting the geographical distributions of these cicadas revealed that each of the P. annulata song types have independent geographical distributions, with relatively small areas of overlap. ‘Predicted distribution’ modelling revealed that the distribution of each song type forms a unique climatic envelope, which suggests that abiotic factors (rather than interactions among the cicadas themselves) influence the geographical representation of the different song types. One song type has consistent differences in male genitalia, and female ovipositor length differs significantly among three of the other song types. Each song type is strongly associated with a small number of tree species, and these associations are maintained in areas of sympatry. The spatial comparisons made in this study suggest that the P. annulata song types investigated actually represent three species. One of these species is represented by two of the song types originally recognized, and these appear to intergrade in sympatry, and thus represent subspecies. The spatial consistency of the plant associations and morphology exhibited by these (sub)species is significant because it represents an ecological measure of species stability. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 101 , 553–565.     

Diversity in the surface morphology of adjacent epithelial cells of the choroid plexus: an ultrastructural analysis

It is generally known that the luminal surface of the choroidal epithelial cells is covered with a luxuriant coat of slender microvilli and cilia. However, extensive ultrastructural studies on the surface morphology of choroidal epithelial cells are lacking. This study, therefore, is focused on the detailed surface morphology of the choroid plexus of the lateral ventricle of adult Wistar rats using transmission and scanning electron microscopy. The animals were anesthetized, perfused with 0.9% oxygenated saline followed by 3% gluteraldehyde and the choroid plexus was processed for routine electron microscopy. The results of the ultrastructural observations presented in this study show that even the neighboring choroidal epithelial cells may express distinct morphology. In addition to the usually described morphology of choroidal epithelial cells, in this study, the presence of cells with uniform small blebs, crenulated or doughnut shaped structures, large mature blebs, or cells with an extensive network of fibers were observed. Although, dissimilar surface morphology of adjacent choroidal epithelial cells may indicate their distinct functional status, further studies are necessary to understand the physiological relevance of the varied surface morphology of choroidal epithelial cells.     

Effects of an invasive species on refuge‐site selection by native fauna: The impact of cane toads on native frogs in the Australian tropics

Invasive species can induce shifts in habitat use by native taxa: either by modifying habitat availability, or by repelling or attracting native species to the vicinity of the invader. The ongoing invasion of cane toads (Rhinella marina) through tropical Australia might affect native frogs by affecting refuge‐site availability, because both frogs and toads frequently shelter by day in burrows. Our laboratory and field studies in the wet‐dry tropics show that native frogs of at least three species (Litoria tornieri, Litoria nasuta and Litoria dahlii) preferentially aggregate with conspecifics, and with (some) other species of native frogs. However, the frogs rarely aggregated with cane toads either in outdoor arenas or in standardized experimental burrows that we monitored in the field. The native frogs that we tested either avoided burrows containing cane toads (or cane toad scent) or else ignored the stimulus (i.e. treated such a burrow in the same way as they did an empty burrow). Native frogs selected a highly non‐random suite of burrows as diurnal retreat sites, whereas cane toads were less selective. Hence, even in the absence of toads, frogs do not use many of the burrows that are suitable for toads. The invasion of cane toads through tropical Australia is unlikely to have had a major impact on retreat‐site availability for native frogs.     

Structural motifs for pyridoxal-5'-phosphate binding in decarboxylases: an analysis based on the crystal structure of the Lactobacillus 30a ornithine decarboxylase.

Two of the five domains in the structure of the ornithine decarboxylase (OrnDC) from Lactobacillus 30a share similar structural folds around the pyridoxal-5''-phosphate (PLP)-binding pocket with the aspartate aminotransferases (AspATs). Sequence comparisons focusing on conserved residues of the aligned structures reveal that this structural motif is also present in a number of other PLP-dependent enzymes including the histidine, dopa, tryptophan, glutamate, and glycine decarboxylases as well as tryptophanase and serine-hydroxymethyl transferase. However, this motif is not present in eukaryotic OrnDCs, the diaminopimelate decarboxylases, nor the Escherichia coli or oat arginine decarboxylases. The identification and comparison of residues involved in defining the different classes are discussed.