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PubMed2024

Adaptive or non-adaptive? Cranial evolution in a radiation of miniaturized day geckos.

Lygodactylus geckos represent a well-documented radiation of miniaturized lizards with diverse life-history traits that are widely distributed in Africa, Madagascar, and South America. The group has diversified into numerous species with high levels of morphological similarity. The evolutionary processes underlying such diversification remain enigmatic, because species live in different ecological biomes, ecoregions and microhabitats, while suggesting strikingly high levels of homoplasy. To underscore this evolutionary pattern, here we explore the shape variation of skull elements (i.e., cranium, jaw and inner ear) using 3D geometric morphometrics and phylogenetic comparative methods on computed tomography scans (CT-scan) of a sample encompassing almost all recognized taxa within Lygodactylus. The results of this work show that skull and inner ear shape variation is low (i.e., there is high overlapping on the morphospace) across geographic regions, macrohabitats and lifestyles, implying extensive homoplasy. Furthermore, we also found a strong influence of allometry shaping cranial variation both at intra and interspecific levels, suggesting a major constraint underlying skull architecture, probably as a consequence of its miniaturization. The remaining variation that is not allometric is independent of phylogeny and ecological adaptation and can probably be interpreted as the result of intrinsic developmental plasticity. This, in turn, supports the interpretation that speciation in this group is largely concordant with a non-adaptive hypothesis, which results mainly from vicariant processes.

Animals↗
PubMed2004

Experimental evidence for sympatric ecological diversification due to frequency-dependent competition in Escherichia coli.

We investigate adaptive diversification in experimental Escherichia coli populations grown in serial batch cultures on a mixture of glucose and acetate. All 12 experimental lines were started from the same genetically uniform ancestral strain but became highly polymorphic for colony size after 1000 generations. Five populations were clearly dimorphic and thus serve as a model for an adaptive lineage split. We analyzed the ecological basis for this dimorphism by studying bacterial growth curves. All strains exhibit diauxie, that is, sequential growth on the two resources. Thus, they exhibit phenotypic plasticity, using mostly glucose when glucose is abundant, then switching to acetate when glucose concentration is low. However, the coexisting strains differ in their diauxie pattern, with one cluster in the dimorphic populations growing better in the glucose phase, and the other cluster having a much shorter lag when switching to the acetate phase. Using invasion experiments, we show that the dimorphism of these two ecological types is maintained by frequency-dependent selection. Using a mathematical model for the adaptive dynamics of diauxie behavior, we show that evolutionary branching in diauxie behavior is a plausible theoretical scenario. Our results support the hypothesis that, in our experiments, adaptive diversification from a genetically uniform ancestor occurred due to frequency-dependent ecological interactions. Our results have implications for understanding the evolution of cross-feeding polymorphism in microorganisms, as well as adaptive speciation due to frequency-dependent selection on phenotypic plasticity.

Adaptation, Physiological↗
PubMed2003

Contrasting patterns of radiation in African and Australian Restionaceae.

The floras of the Mediterranean-climate areas of southern Africa and southwestern Australia are remarkably species rich. Because the two areas are at similar latitudes and in similar positions on their respective continents, they have probably had similar Cenozoic climatic histories. Here we test the prediction that the evolution of the species richness in the two areas followed a similar temporal progression by comparing the rates of lineage accumulation for African and Australian Restionaceae. Restionaceae (Poales) are typical and often dominant elements in the fynbos vegetation of the Cape Floristic Region of southern Africa and the kwongan vegetation of the Southwestern Floristic Province of Western Australia. The phylogeny of the family was estimated from combined datasets for rbcL and trnL-F sequences and a large morphological dataset; these datasets are largely congruent. The monophyly of Restionaceae is supported and a basal division into an African clade (approximately 350 species) and an Australian clade (146 species) corroborated. There is also support for a futher subdivision of these two large sister-clades, but the terminal resolution within the African clade is very weak. Fossil pollen records provided a minimum age of the common ancestor of Australian and African Restionaceae as 64-71 million years ago, and this date was used to calibrate a molecular clock. A molecular clock was rejected by a likelihood ratio test; therefore, rate changes between the lineages were smoothed using nonparametric rate smoothing. The rate-corrected ages were used to construct a plot of lineages through time. During the Palaeogene the Australian lineage diversity increased consistent with the predictions of the constant birthrate model, while the African lineage diversity showed a dramatic increase in diversification rate in the Miocene. Incomplete sampling obscures the patterns in the Neogene, but extending the trends to the modern extant diversity suggests that this acceleration in the speciation rate continued in the African clade, whereas the Australian clade retained a constant diversification rate. The substantial morphological and anatomical similarity between the African and Australian Restionaceae appear to preclude morphological innovations as possible explanations for the intercontinental differences. Most likely these differences are due to the greater geographical extent and ecological variation in temperate Australia than temperate Africa, which might have provided refugia for basal Restionaceae lineages, whereas the more mountainous terrain of southern Africa might have provided the selective regimes for a more rapid, recent speciation.

Africa↗
PubMed2005

Genomic insights that advance the species definition for prokaryotes.

To help advance the species definition for prokaryotes, we have compared the gene content of 70 closely related and fully sequenced bacterial genomes to identify whether species boundaries exist, and to determine the role of the organism's ecology on its shared gene content. We found the average nucleotide identity (ANI) of the shared genes between two strains to be a robust means to compare genetic relatedness among strains, and that ANI values of approximately 94% corresponded to the traditional 70% DNA-DNA reassociation standard of the current species definition. At the 94% ANI cutoff, current species includes only moderately homogeneous strains, e.g., most of the >4-Mb genomes share only 65-90% of their genes, apparently as a result of the strains having evolved in different ecological settings. Furthermore, diagnostic genetic signatures (boundaries) are evident between groups of strains of the same species, and the intergroup genetic similarity can be as high as 98-99% ANI, indicating that justifiable species might be found even among organisms that are nearly identical at the nucleotide level. Notably, a large fraction, e.g., up to 65%, of the differences in gene content within species is associated with bacteriophage and transposase elements, revealing an important role of these elements during bacterial speciation. Our findings are consistent with a definition for species that would include a more homogeneous set of strains than provided by the current definition and one that considers the ecology of the strains in addition to their evolutionary distance.

Bacteria↗
PubMed2026

Accounting for recombination rate variation improves inference of barrier loci and reveals the role of both natural and sexual selection in an incipient bird radiation.

Examining genomic patterns of differentiation across lineage pairs at different stages of the speciation continuum, in combination with recombination maps, can help disentangle the effects of linked and divergent selection and identify lineage-specific targets of selection that may act as barrier loci during speciation. Here, we apply this framework to genomic data from African and Indian Ocean bird species of the genus Zosterops (Zosteropidae) to identify candidate barrier loci between ecologically, phenotypically, and genetically distinct Reunion gray white-eye (Zosterops borbonicus) parapatric geographic forms. Using analyses that account for recombination rate variation, we show that putative targets of divergent selection are primarily located on the Z chromosome, except in comparisons between geographic forms that differ in their ecologies. Functional annotation revealed that candidate barrier loci between forms with similar environmental niches are associated with genes involved in song formation and immune function, whereas those between forms with different environmental niches are associated with adaptation to altitude, morphology, and song behavior. Our results highlight the combined roles of natural and sexual selection in the evolution of reproductive barriers in this incipient species radiation.

Animals↗
PubMed2001

Divergent sexual selection enhances reproductive isolation in sticklebacks.

Sexual selection may facilitate speciation because it can cause rapid evolutionary diversification of male mating signals and female preferences. Divergence in these traits can then contribute to reproductive isolation. The sensory drive hypothesis predicts that three mechanisms underlie divergence in sexually selected traits: (1) habitat-specific transmission of male signals; (2) adaptation of female perceptual sensitivity to local ecological conditions; and (3) matching of male signals to female perceptual sensitivity. I test these mechanisms in threespine sticklebacks (Gasterosteus spp.) that live in different light environments. Here I show that female perceptual sensitivity to red light varies with the extent of redshift in the light environment, and contributes to divergent preferences. Male nuptial colour varies with environment and is tuned to female perceptual sensitivity. The extent of divergence among populations in both male signal colour and female preference for red is correlated with the extent of reproductive isolation in these recently diverged species. These results demonstrate that divergent sexual selection generated by sensory drive contributes to speciation.

Animals↗
PubMed2006

Patterns of diversification of Afrotropical Otiteselline fig wasps: phylogenetic study reveals a double radiation across host figs and conservatism of host association.

We studied the phylogenetic relationships of Otiteselline fig waSPS associated with Ficus in the Afrotropical region using rDNA sequences. African fig species usually host two species of Otiteselline fig waSPS. Phylogenetic analyses reveal that this pattern of association results from the radiation of two clades of waSPS superimposed on the fig system. Within each clade, wasp species generally cluster according to their host classification. The phylogenies of the two clades are also generally more congruent than expected by chance. Together these results suggest that Otiteselline wasp speciation is largely constrained by the diversification of their hosts. Finally, we show a difference in ovipositor length between the two Otiteselline species coexisting in the same Ficus species, which probably corresponds to ecological differences. The diversification of ecological niches within the fig is probably, with cospeciation, one of the key factors explaining the diversification and maintenance of species of parasites of the fig/pollinator system.

Animals↗
PubMed2004

Are viruses driving microbial diversification and diversity?

Viruses can influence the genetic diversity of prokaryotes in various ways. They can affect the community composition of prokaryotes by 'killing the winner' and keeping in check competitive dominants. This may sustain species richness and the amount of information encoded in genomes. Viruses can also transfer (viral and host) genes between species. Such mechanisms have probably influenced the speciation of prokaryotes. Whole-genome sequencing has clearly revealed the importance of (virus-mediated) gene transfer. However, its significance for the ecological performance of aquatic microbial communities is only poorly studied, although the few available reports indicate a large potential. Here, we present data supporting the hypothesis that viral genes and viral activity generate genetic variability of prokaryotes and are a driving force for ecological functioning and evolutionary change.

Bacteria↗
PubMed2005

Molecular phylogenetics of the Macaronesian-endemic genus Bystropogon (Lamiaceae): palaeo-islands, ecological shifts and interisland colonizations.

Abstract A molecular phylogenetic study of Bystropogon L'Her. (Lamiaceae) is presented. We performed a cladistic analysis of nucleotide sequences of the internal transcribed spacers (ITS), of the nuclear ribosomal DNA, and of the trnL gene and trnL-trnF intergenic spacer of the chloroplast DNA. Bystropogon odoratissimus is the only species endemic to the Canary Islands that occurs in the three palaeo-islands of Tenerife. This species is not part of an early diverging lineage of Bystropogon and we suggest that it has a recent origin. This phylogenetic pattern is followed by most of the species endemic to the palaeo-islands of Tenerife. The two sections currently recognized in Bystropogon form two monophyletic groups. Taxa belonging to the section Bystropogon clade show interisland colonization limited to the Canary Islands with ecological shifts among three ecological zones. Taxa from the section Canariense clade show interisland colonization both within the Canary Islands and between the Canary Islands and Madeira. Speciation events within this clade are mostly limited to the laurel forest. The genus has followed a colonization route from the Canaries towards Madeira. This route has also been followed by at least five other plant genera with species endemic to Macaronesia. Major incongruences were found between the current infrasectional classification and the molecular phylogeny, because the varieties of Bystropogon origanifolius and Bystropogon canariensis do not form two monophyletic groups. The widespread B. origanifolius appears as progenitor of the other species in section Bystropogon with a more restricted distribution.

DNA, Chloroplast↗
PubMed2005

Speciation of mercury and mode of transport from placer gold mine tailings.

Historic placer gold mining in the Clear Creek tributary to the Sacramento River (Redding, CA) has highly impacted the hydrology and ecology of an important salmonid spawning stream. Restoration of the watershed utilized dredge tailings contaminated with mercury (Hg) introduced during gold mining, posing the possibility of persistent Hg release to the surrounding environment, including the San Francisco Bay Delta. Column experiments have been performed to evaluate the extent of Hg transport under chemical conditions potentially similar to those in river restoration projects utilizing dredge tailings such as at Clear Creek. Physicochemical perturbations, in the form of shifts in column influent ionic strength and the presence of a low molecular weight organic acid, were applied to coarse and fine sand placer tailings containing 109-194 and 69-90 ng of Hg/g, respectively. Significant concentrations of mercury, up to 16 microg/L, leach from these sediments in dissolved and particle-associated forms. Sequential chemical extractions (SCE) of these tailings indicate that elemental Hg initially introduced during gold mining has been transformed to readily soluble species, such as mercury oxides and chlorides (3-4%), intermediately extractable phases that likely include (in)organic sorption complexes and amalgams (75-87%), and fractions of highly insoluble forms such as mercury sulfides (6-20%; e.g., cinnabar and metacinnabar). Extended X-ray absorption fine structure (EXAFS) spectroscopic analysis of colloids obtained from column effluent identified cinnabar particles as the dominant mobile mercury-bearing phase. The fraction of intermediately extractable Hg phases also likely includes mobile colloids to which Hg is adsorbed.

California↗
PubMed1989

Comparative physiology and biochemistry: challenges for the future.

1. Comparative physiology is distinguished from other types of physiology by treating the diversity of solutions of functional problems and by using kind of animal as a functional variable. 2. The strength of comparative physiology os its capacity to give some solutions to problems in basic biology. 3. Specific examples of subject areas to which comparative physiology contributes are: (a) mechanisms underlying evolution; (b) the nature of speciation; (c) comparative cognitive science, neural models for behavior; and (d) applications of molecular techniques to physiology of whole animals. 4. Applications continue in ecology, medicine and agriculture. 5. The breadth of the comparative approach to physiology has important philosophical implications.

Animals↗
PubMed1993

Ecological separation and genetic isolation of Neisseria gonorrhoeae and Neisseria meningitidis.

BACKGROUND: Classifying bacteria into species is problematic. Most microbiologists consider species to be groups of isolates that share some arbitrary degree of relatedness of biochemical or molecular (such as DNA sequence) features and that, ideally, are clearly delineated from all other groups of isolates. The main problem in applying to bacteria a biological concept of species based on the ability or inability of their genes to recombine, is that recombination appears to be rare in bacteria in nature, as indicated by the strong linkage disequilibrium between alleles found in most bacterial populations. However, there are some naturally transformable bacteria in which assortative recombination appears to be so frequent that alleles are in, or close to, linkage equilibrium. For these recombining populations a biological concept of species might be applicable. RESULTS: Populations of Neisseria gonorrhoeae and Neisseria meningitidis from Spain were analysed by multilocus enzyme electrophoresis. The data indicate that assortative recombination occurs frequently within populations, but not between populations. Similarly, the sequences of two house-keeping genes show no evidence of intragenic recombination between N. gonorrhoeae and N. meningitidis. CONCLUSIONS: N. gonorrhoeae and N. meningitidis represent extremely closely related 'sexual' populations that appear to be genetically isolated in nature, and thus conform to the biological concept of species. The extreme uniformity of N. gonorrhoeae house-keeping genes suggests that this species may have arisen recently as a clone of N. meningitidis that could colonize the genital tract. Ecological isolation - of populations that can colonize the genital tract from those that can colonize the nasopharynx - may have been an important component in speciation, leading to a lower frequency of recombination between species than within species.

Journal Article↗
PubMed2003

Developmental stability and adaptive variability of male genitalia in sexually dimorphic beetles.

Animal genitalia often show distinct developmental and evolutionary relationships with other parts of the body. Morphological observations of 29 sexually dimorphic and monomorphic beetle species in 16 genera of families Scarabaeidae and Lucanidae, Coleoptera, in 53 locations revealed that male genitalia size was consistently and distinctly less variable than that of other body parts within the same population, while it differentiated more readily among different populations than other body parts. The most noticeable genitalia size differentiation occurred in populations that coexisted with morphologically and ecologically similar congeneric species. Such differentiation may indicate selection for reproductive isolation. These characteristics of genitalia morphology may have been instrumental in generating the speciation pattern seen in most beetles.

Animals↗
PubMed2002

Ecologic niche modeling and differentiation of populations of Triatoma brasiliensis neiva, 1911, the most important Chagas' disease vector in northeastern Brazil (hemiptera, reduviidae, triatominae).

Ecologic niche modeling has allowed numerous advances in understanding the geographic ecology of species, including distributional predictions, distributional change and invasion, and assessment of ecologic differences. We used this tool to characterize ecologic differentiation of Triatoma brasiliensis populations, the most important Chagas' disease vector in northeastern Brazil. The species' ecologic niche was modeled based on data from the Fundação Nacional de Saúde of Brazil (1997-1999) with the Genetic Algorithm for Rule-Set Prediction (GARP). This method involves a machine-learning approach to detecting associations between occurrence points and ecologic characteristics of regions. Four independent "ecologic niche models" were developed and used to test for ecologic differences among T. brasiliensis populations. These models confirmed four ecologically distinct and differentiated populations, and allowed characterization of dimensions of niche differentiation. Patterns of ecologic similarity matched patterns of molecular differentiation, suggesting that T. brasiliensis is a complex of distinct populations at various points in the process of speciation.

Animals↗
PubMed2005

Intraparental gamete competition provides a selective advantage for the development of hybrid sterility via meiotic drive.

Hybrid sterility can have evolutionary significance and varies substantially by taxon, but few models attempt to predict or explain this variability. Hybrid sterility is commonly observed and develops early in isolation, at odds with straightforward models that predict it would develop slowly and rarely be seen. Meiotic drive might explain the rapid development of hybrid sterility, but drive is rarely observed, modifiers are expected to repress it, and no precise testable predictions are available. Here I develop population genetic models for the establishment of meiotic drive based on how it spreads by benefiting carrier gametes competing with noncarrier gametes from the same parent, or intraparental gamete competition. The resulting models predict that meiotic drive can often produce substantial hybrid sterility over time even in the presence of repressors, yet observable drive will be rare. They also make quantitative predictions of the degree of sterility based on observable parameters of reproductive ecology, including frequency of multiple mating, effective dispersal of offspring, and population size. Finally, they suggest explanations for the association of heterochromatin changes with speciation. Experimental evidence is discussed showing that drive alleles at least sometimes contribute to hybrid sterility.

Computer Simulation↗
PubMed2005

Ecological adaptation and species recognition drives vocal evolution in neotropical suboscine birds.

Given that evolutionary divergence in mating signals leads to reproductive isolation in numerous animal taxa, understanding what drives signal divergence is fundamental to our understanding of speciation. Mating signals are thought to diverge via several processes, including (1) as a by-product of morphological adaptation, (2) through direct adaptation to the signaling environment, or (3) to facilitate species recognition. According to the first two hypotheses, birdsongs diversify in different foraging niches and habitats as a product of selection for optimal morphology and efficient sound transmission, respectively. According to the third hypothesis, they diversify as a result of selection against maladaptive hybridization. In this study I test all three hypotheses by examining the influence of morphology, acoustic environment, and the presence of closely related congeners on song structure in 163 species of antbird (Thamnophilidae). Unlike oscine passerines, these Neotropical suboscines make ideal subjects because they develop their songs without learning. In other words, patterns of vocal divergence are not complicated by cultural evolution. In support of the morphological adaptation hypothesis, body mass correlates with the acoustic frequency of songs, and bill size with temporal patterning. These relationships were robust, even when controlling for phylogenetic inertia using independent contrasts, suggesting that there has been correlated evolution between morphological and acoustic traits. The results also support the acoustic adaptation hypothesis: birds which habitually sing in the understory and canopy produce higher-pitched songs than those that sing in the midstory, suggesting that song structure is related to the sound transmission properties of different habitat strata. Finally, the songs of sympatric pairs of closely related species are more divergent than those of allopatric pairs, as predicted by the species recognition hypothesis. To my knowledge, these data provide the first direct evidence that species recognition and ecological adaptation operate in tandem, and that the interplay between these factors drives the evolution of mating signals in suboscine birds.

Acoustics↗
PubMed2025

Repeatable Genomic Outcomes Along the Speciation Continuum: Insights From Pine Hybrid Zones (Genus Pinus).

Hybridization is a widespread evolutionary process and a key source of evolutionary novelty. Despite intensive study, the extent to which hybridization is deterministic and repeatable, particularly in recurrent contact events involving the same species under varying ecological conditions, remains unclear. Here, we investigated three replicated contact zones between Scots pine (Pinus sylvestris) and dwarf mountain pine (Pinus mugo) in Central Europe: two occurring in peatland habitats and one in a contrasting sandstone outcrop. Using genome-wide SNP genotyping of over 1300 individuals, we analysed genomic structure, diversity, and ancestry patterns across these zones. All sites revealed pervasive hybridization, dominated by later-generation hybrids and a notable scarcity of pure P. mugo. Across environments, hybrid populations exhibited strikingly consistent genomic compositions, with asymmetric introgression strongly biased toward P. mugo ancestry, suggesting that hybrid genome structure may follow predictable patterns under similar ecological conditions and could be shaped by cytonuclear incompatibilities. Nonetheless, we also detected site-specific differences in hybrid diversity and phenotype, highlighting the influence of local environmental selection on shared hybrid genomic backgrounds. We provide genomic evidence that Pinus uliginosa, a morphologically distinct peat bog pine traditionally regarded as a relict and endangered species is instead a partially stabilised hybrid lineage. Its genome reflects incomplete hybridization and ecological filtering, yet it lacks sufficient genetic divergence to be recognised as a distinct species. Together, these results provide evidence for the repeatability of hybridization processes, which result in the formation of phenotypes reflecting a species continuum subjected to strong environmental pressures. The findings support the simplification of taxonomic nomenclature within the Pinus mugo complex, informing adaptive conservation strategies and the genetic management of hybrid lineages.

Hybridization, Genetic↗