Speciation Events Research Articles

Mitochondrial phylogeny of the brittle star genus Ophioderma

We reconstructed the mitochondrial phylogeny of the species of the brittle star genus Ophioderma, using sequences of the Cytochrome Oxidase I gene (COI) to address four questions: (i) Are the species of Ophioderma described on morphological evidence reflected in mitochondrial genealogy? (ii) Which species separated from which? (iii) When did speciation events occur? (iv) What is the rate of COI evolution in ophiuroids? We found that most of the 22 described species we sampled coincide with monophyletic clusters of COI sequences, but there are exceptions, most notably in the eastern Pacific, in which three undescribed species were indicated. The COI phylogeny lacks resolution in the deeper nodes, but it does show that there are four species pairs, the members of which are found on either side of the central American Isthmus. Two pairs with a genetic distance of ~ 4% between Atlantic and Pacific members were probably split during the final stages of Isthmus completion roughly 3 million years ago. The rate of divergence provided by these pairs allowed the calibration of a relaxed molecular clock. Estimated dates of divergence indicate that the lineages leading to extant species coalesce at times much older than congeneric species in other classes of echinoderms, suggesting that low extinction rates may be one of the reasons that ophiuroids are species-rich. The mean rate of COI substitution in Ophioderma is three times slower than that of echinoids. Conclusions of previous mitochondrial DNA studies of ophiuroids that relied on echinoid calibrations to determine divergence times need to be revised.

Biogeographic and evolutionary history of Crotonoideae based on pollen evidence from Indian Late Cretaceous and Paleogene sediments

AbstractEuphorbiaceae Juss. is a globally distributed angiosperm family with considerable diversity. It is divided into five subfamilies, each of which possesses pollen of distinct morphology. The subfamily Crotonoideae, occurring in evergreen, moist deciduous as well as dry deciduous forests of the world, shows a disjunct distribution pattern in Gondwana and Southeast Asia. This subfamily underwent multiple speciation and extinction events during the northward voyage of the Indian Plate during the Late Cretaceous‐early Paleogene. We studied Crotonoideae fossil pollen from the Late Cretaceous Deccan Intertrappeans (Central India) and early Paleogene sediments from the western Indian lignite mines, and as a result, report 10 pollen fossils showing similarity with the extant genera Blachia, Croton, Endospermum, Jatropha, Klaineanthus, and Tetrorchidium, representing 4 tribes of Crotonoideae viz. Adenoclineae, Codiaeae, Crotoneae, and Jatropheae. Fossil evidences from the present study suggest a Gondwanan origin for Crotonoideae. Based on the extant and fossil species, Africa could be the place of origin for most of the Crotonoideae lineages that later dispersed to India via the Kohistan‐Ladakh Island Arc during the late Maastrichtian‐Paleocene time. The former distribution of Crotonoideae in mid‐high latitudinal regions is due to the dispersal of the subfamily from Africa to mid latitudinal regions of northern hemisphere during the early Paleogene via the boreotropical dispersal route. This study also corroborates the “Out of India” hypothesis for the dispersal of Crotonoideae from India to Southeast Asia. The present deep‐time fossil records from India discussed in this study substantiate the evolutionary and biogeographic history of subfamily Crotonoideae.

Pronounced mito-nuclear discordance and various Wolbachia infections in the water ringlet Erebia pronoe have resulted in a complex phylogeographic structure

Several morphological and mitochondrial lineages of the alpine ringlet butterfly species Erebia pronoe have been described, indicating a complex phylogenetic structure. However, the existing data were insufficient and allow neither a reconstruction of the biogeographic history, nor an assessment of the genetic lineages. Therefore, we analysed mitochondrial (COI, NDI) and nuclear (EF1α, RPS5) gene sequences and compared them with sequences from the sister species Erebia melas. Additionally, we combined this information with morphometric data of the male genitalia and the infection patterns with Wolbachia strains, based on a WSP analysis. We obtained a distinct phylogeographic structure within the E. pronoe-melas complex with eight well-distinguishable geographic groups, but also a remarkable mito-nuclear discordance. The mito-nuclear discordance in E. melas and E. pronoe glottis can be explained by different ages of Wolbachia infections with different Wolbachia strains, associated selective sweeps, and hybridisation inhibition. Additionally, we found indications for incipient speciation of E. pronoe glottis in the Pyrenees and a pronounced range dynamic within and among the other high mountain systems of Europe. Our results emphasize the importance of combined approaches in reconstructing biogeographic patterns and evaluating phylogeographic splits.

Modeling the Process of Speciation Using a Multiscale Framework Including A Posteriori Error Estimates

This paper concerns the modeling and numerical simulation of the process of speciation. In particular, given conditions for which one or more speciation events within an ecosystem occur, our aim is to develop the necessary modeling and simulation tools. Care is also taken to establish a solid mathematical foundation on which our modeling framework is built. This is the subject of the first half of the paper. The second half is devoted to developing a multiscale framework for eco-evolutionary modeling, where the relevant scales are that of species and individual/population, respectively. The species level model we employ can be considered as an extension of the classical Lotka--Volterra model, where in addition to the species abundance, the model also governs the evolution of the species mean traits and species trait covariances and in this sense generalizes the purely ecological Lotka--Volterra model to an eco-evolutionary model. Although the model thus allows for evolving species, it does not (by construction) allow for the branching of species, i.e., speciation events. The reason for this is related to that of separate scales; the unit of species is too coarse to capture the fine-scale dynamics of a speciation event. Instead, the branching species should be regarded as a population of individuals moving along a selection of trait axes (i.e., trait-space). For this, we employ a trait-specific population density model governing the dynamics of the population density as a function of evolutionary traits. At this scale there is no a priori definition of species, but both species and speciation may be defined a posteriori as, e.g., local maxima and saddle points of the population density, respectively. Hence, a system of interacting species can be described at the species level, while for branching species a population level description is necessary. Our multiscale framework thus consists of coupling the species and population level models where speciation events are detected in advance and then resolved at the population scale until the branching is complete. Moreover, since the population level model is formulated as a PDE, we first establish the well-posedness in the time-discrete setting and then derive the a posteriori error estimates, which provides a fully computable upper bound on an energy-type error, including also for the case of general smooth distributions (which will be useful for the detection of speciation events). Several numerical tests validate our framework in practice.

Population genomic consequences of life-history and mating system adaptation to a geothermal soil mosaic in yellow monkeyflowers.

Local selection can promote phenotypic divergence despite gene flow across habitat mosaics, but adaptation itself may generate substantial barriers to genetic exchange. In plants, life-history, phenology, and mating system divergence have been proposed to promote genetic differentiation in sympatry. In this study, we investigate phenotypic and genetic variation in Mimulus guttatus (yellow monkeyflowers) across a geothermal soil mosaic in Yellowstone National Park (YNP). Plants from thermal annual and nonthermal perennial habitats were heritably differentiated for life-history and mating system traits, consistent with local adaptation to the ephemeral thermal-soil growing season. However, genome-wide genetic variation primarily clustered plants by geographic region, with little variation sorting by habitat. The one exception was an extreme thermal population also isolated by a 200 m geographical gap of no intermediate habitat. Individual inbreeding coefficients (FIS ) were higher (and predicted by trait variation) in annual plants and annual pairs showed greater isolation by distance at local (<1 km) scales. Finally, YNP adaptation does not reuse a widespread inversion that underlies M. guttatus life-history ecotypes range-wide, suggesting a novel genetic mechanism. Overall, this work suggests that life-history and mating system adaptation strong enough to shape individual mating patterns does not necessarily generate incipient speciation without geographical barriers.

Inferring the genome-wide history of grasses

Establishing the relationships among organisms is fundamental to numerous fields in biology, including systematics, evolutionary biology, and epidemiology. These relationships are represented via phylogenetic trees, which depict the history of genes and capture both speciation and gene duplication events. When multiple genes are analyzed simultaneously, the history of the genomes and the species that bear them can be reconstructed, as well as episodes of genetic exchanges among lineages. The genomics revolution and analytical advancements have led to large-scale genome-wide phylogenies resolving the history of an increasing number of taxonomic groups and revealing in some cases complex histories of hybridization.

Conservation Genetics of Mediterranean Brown Trout in Central Italy (Latium): A Multi-Marker Approach

Brown trout is considered a complex of incipient species, including several phylogenetic lineages, whose natural distribution in the Mediterranean area has been altered, since the beginning of the 1900s, by massive introductions of domestic strains of Atlantic origin to support fisheries. Introduced trout naturalize in new suitable environments and extensively hybridize with native populations. Here, we characterized putatively neutral and adaptive genetic variability and population structure of Mediterranean brown trout from six river catchments in central peninsular Italy, as revealed by both mitochondrial (Control Region) and nuclear (microsatellites, LDH-C1, major histocompatibility complex) markers. We quantified the admixture of wild populations with hatchery strains and evaluated the effects of domestic trout introductions on shaping population genetics. Our analyses indicated: (1) a composite picture of genetic variability in the area, with the presence of all native Mediterranean trout mitochondrial lineages (“Adriatic”, “Mediterranean”, “marmoratus”), various frequencies of allochthonous genotypes and different rates of introgression among sampling sites; (2) asymmetric mito-nuclear introgression; (3) increasing nuclear marker diversity with increasing levels of admixture across populations; (4) strong population structure coupled with relatively low effective population size. Data allowed the identification of five management units and we propose specific actions to support ongoing and future conservation strategies within the examined area.

Populational Differentiation in Boana bischoffi (Anura, Hylidae): Revisiting the Issue Using Molecular, Morphological, and Acoustic Data

Boana bischoffi was originally described from the Brazilian state of Rio Grande do Sul and has Boana multilineata from São Paulo as a junior synonym. The history of its nomenclature reflects the varying interpretation of the dorsal color pattern of the two different populations. We reevaluate the problem of taxonomic recognition of Boana multilineata based on molecular, morphometric, and acoustic data. The molecular data revealed two major clades that are partially concordant with the morphological and acoustic differentiation. Morphometric analyses revealed elements of differentiation between populations in snout–vent length (SVL) and head shape, which were patterns not detected previously. Discrimination considering call features was substantial, even complete in a discriminant analysis. Despite these differences, we refrain from resurrecting the name B. multilineata due to the existence of putative introgression zones, the effect of SVL in call dominant frequency, and lack of taxonomically relevant differences. Boana bischoffi might represent a case of incipient speciation.

Diversity and Evolution of Pigment Types in Marine Synechococcus Cyanobacteria.

Synechococcus cyanobacteria are ubiquitous and abundant in the marine environment and contribute to an estimated 16% of the ocean net primary productivity. Their light-harvesting complexes, called phycobilisomes (PBS), are composed of a conserved allophycocyanin core, from which radiates six to eight rods with variable phycobiliprotein and chromophore content. This variability allows Synechococcus cells to optimally exploit the wide variety of spectral niches existing in marine ecosystems. Seven distinct pigment types or subtypes have been identified so far in this taxon based on the phycobiliprotein composition and/or the proportion of the different chromophores in PBS rods. Most genes involved in their biosynthesis and regulation are located in a dedicated genomic region called the PBS rod region. Here, we examine the variability of gene content and organization of this genomic region in a large set of sequenced isolates and natural populations of Synechococcus representative of all known pigment types. All regions start with a tRNA-PheGAA and some possess mobile elements for DNA integration and site-specific recombination, suggesting that their genomic variability relies in part on a “tycheposon”-like mechanism. Comparison of the phylogenies obtained for PBS and core genes revealed that the evolutionary history of PBS rod genes differs from the core genome and is characterized by the co-existence of different alleles and frequent allelic exchange. We propose a scenario for the evolution of the different pigment types and highlight the importance of incomplete lineage sorting in maintaining a wide diversity of pigment types in different Synechococcus lineages despite multiple speciation events.

Orphan gene in Littorina: An unexpected role of symbionts in the host evolution

Mechanisms of reproductive isolation between closely related sympatric species are of high evolutionary significance as they may function as initial drivers of speciation and protect species integrity afterwards. Proteins involved in the establishment of reproductive barriers often evolve fast and may be key players in cessation of gene flow between the incipient species. The five Atlantic Littorina (Neritrema) species represent a notable example of recent radiation. The geographic ranges of these young species largely overlap and the mechanisms of reproductive isolation are poorly understood. In this study, we performed a detailed analysis of the reproductive protein LOSP, previously identified in Littorina. We showed that this protein is evolutionary young and taxonomically restricted to the genus Littorina. It has high sequence variation both within and between Littorina species, which is compatible with its presumable role in the reproductive isolation. The strongest differences in the LOSP structure were detected between Littorina subgenera with distinctive repetitive motifs present exclusively in the Neritrema species, but not in L. littorea. Moreover, the sequence of these repetitive structural elements demonstrates a high homology with genetic elements of bacteria, identified as components of Littorina associated microbiomes. We suggest that these elements were acquired from a symbiotic bacterial donor via horizontal genetic transfer (HGT), which is indirectly confirmed by the presence of multiple transposable elements in the LOSP flanking and intronic regions. Furthermore, we hypothesize that this HGT-driven evolutionary innovation promoted LOSP function in reproductive isolation, which might be one of the factors determining the intensive cladogenesis in the Littorina (Neritrema) lineage in contrast to the anagenesis in the L. littorea clade.

Identification of a novel gene required for competitive growth at high temperature in the thermotolerant yeast Kluyveromyces marxianus.

It is important to understand the basis of thermotolerance in yeasts to broaden their application in industrial biotechnology. The capacity to run bioprocesses at temperatures above 40 °C is of great interest but this is beyond the growth range of most of the commonly used yeast species. In contrast, some industrial yeasts such as Kluyveromyces marxianus can grow at temperatures of 45 °C or higher. Such species are valuable for direct use in industrial biotechnology and as a vehicle to study the genetic and physiological basis of yeast thermotolerance. In previous work, we reported that evolutionarily young genes disproportionately changed expression when yeast were growing under stressful conditions and postulated that such genes could be important for long-term adaptation to stress. Here, we tested this hypothesis in K. marxianus by identifying and studying species-specific genes that showed increased expression during high-temperature growth. Twelve such genes were identified and 11 were successfully inactivated using CRISPR-mediated mutagenesis. One gene, KLMX_70384, is required for competitive growth at high temperature, supporting the hypothesis that evolutionary young genes could play roles in adaptation to harsh environments. KLMX_70384 is predicted to encode an 83 aa peptide, and RNA sequencing and ribo-sequencing were used to confirm transcription and translation of the gene. The precise function of KLMX_70384 remains unknown but some features are suggestive of RNA-binding activity. The gene is located in what was previously considered an intergenic region of the genome, which lacks homologues in other yeasts or in databases. Overall, the data support the hypothesis that genes that arose de novo in K. marxianus after the speciation event that separated K. marxianus and K. lactis contribute to some of its unique traits.

The flooded habitat adaptation, niche differentiation, and evolution of Myristicaceae trees in the Western Ghats biodiversity hotspot in India

AbstractEnvironmental heterogeneity is considered as one of the main drivers of habitat specialization and niche evolution among tropical plant lineages, and local‐scale habitat specialization promotes niche differentiation among sister taxa. In this study, we examined the degree to which habitat specialization leads to niche differentiation across the distribution range of a given species using five species of the family Myristicaceae native to Western Ghats, India, as an example. In the Western Ghats, Myristicaceae species occur in two main habitat types, namely, freshwater swamps (flooded habitat) and terra firme forest (non‐flooded habitat), distributed across a seasonal flooding gradient. First, we reconstructed the evolutionary history of flooded habitat specialization among global and Western Ghats Myristicaceae by mapping flooded habitat association and traits conferring flood tolerance (e.g., aerial roots) on a dated phylogeny. Then, we investigated climatic niche differences among lineages occupying flooded and terra firme habitats using occurrence data and environmental variables. Our analysis revealed swampy habitat occurrence as the probable ancestral state with subsequent speciation events leading to adaptation to non‐swampy habitats. We also show that traits conferring flood tolerance have evolved independently several times during the evolution of Myristicaceae. Furthermore, phylogenetically distantly related Myristicaceae taxa occupying different habitats (flooded and terra firme habitat) in Western Ghats show significant niche divergence. Overall, the repeated gain of swampy habitat specialization and associated morphological traits and evidence for habitat‐associated climatic niche divergence among Myristicaceae taxa suggest that seasonal flooding may have been an important driver of ecological diversification in this primitive plant family.

Environmental filtering drives assembly of diatom communities over evolutionary time‐scales

AbstractAimEcological communities are structured through the interplay of deterministic assembly processes such as competition and environmental filtering. Whereas the drivers of spatial community structure are frequently studied in extant communities, little is known about the relative importance of assembly processes in response to environmental factors over evolutionary time‐scales. Here, we use an integrative framework to unravel community assembly processes since the inception of a long‐lived lake ecosystem.LocationLake Ohrid.Time periodFrom lake formation 1.36 million years ago to the present.Major taxa studiedPlanktonic diatoms.MethodsWe constructed a dated phylogeny of extant and extinct diatoms and collected trait data for 380 fossil communities to quantify phylogenetic community structure and functional richness and to determine the relative importance of deterministic assembly processes over time. We then used regression analysis to correlate the phylogenetic community structure with palaeoenvironmental and intrinsic biological predictors and to identify primary drivers of assembly processes.ResultsOur results suggest a dense packing of niche space with higher species richness and co‐occurrence of closely related species. There are only two short episodes in the very recent past dominated by distantly related taxa. We found distinct changes in phylogenetic community structure upon speciation or extinction events and an increase in mean community relatedness over time.Main conclusionsOur finding of closely related co‐occurring species implies environmental filtering as the primary assembly mechanism, with a minor but increasingly important role of competition towards the present, driven by evolutionary dynamics. Such an increase in the relative contribution of competition to the assembly of communities in relation to the aging of an insular ecosystem, together with a denser packing of morphospace in the early phase of system ontogeny is compatible with ecological predictions according to the theory of island biogeography.

Using RDNA sequences to define dinoflagellate species

Dinoflagellate species are traditionally defined using morphological characters, but molecular evidence accumulated over the past several decades indicates many morphologically-based descriptions are inaccurate. This recognition led to an increasing reliance on DNA sequence data, particularly rDNA gene segments, in defining species. The validity of this approach assumes the divergence in rDNA or other selected genes parallels speciation events. Another concern is whether single gene rDNA phylogenies by themselves are adequate for delineating species or if multigene phylogenies are required instead. Currently, few studies have directly assessed the relative utility of multigene versus rDNA-based phylogenies for distinguishing species. To address this, the current study examined D1-D3 and ITS/5.8S rDNA gene regions, a multi-gene phylogeny, and morphological characters in Gambierdiscus and other related dinoflagellate genera to determine if they produce congruent phylogenies and identify the same species. Data for the analyses were obtained from previous sequencing efforts and publicly available dinoflagellate transcriptomic libraries as well from the additional nine well-characterized Gambierdiscus species transcriptomic libraries generated in this study. The D1-D3 and ITS/5.8S phylogenies successfully identified the described Gambierdiscus and Alexandrium species. Additionally, the data showed that the D1-D3 and multigene phylogenies were equally capable of identifying the same species. The multigene phylogenies, however, showed different relationships among species and are likely to prove more accurate at determining phylogenetic relationships above the species level. These data indicated that D1-D3 and ITS/5.8S rDNA region phylogenies are generally successful for identifying species of Gambierdiscus, and likely those of other dinoflagellates. To assess how broadly general this finding is likely to be, rDNA molecular phylogenies from over 473 manuscripts representing 232 genera and 863 described species of dinoflagellates were reviewed. Results showed the D1-D3 rDNA and ITS phylogenies in combination are capable of identifying 97% of dinoflagellate species including all the species belonging to the genera Alexandrium, Ostreopsis and Gambierdiscus, although it should be noted that multi-gene phylogenies are preferred for inferring relationships among these species. A protocol is presented for determining when D1-D3, confirmed by ITS/5.8S rDNA sequence data, would take precedence over morphological features when describing new dinoflagellate species. This protocol addresses situations such as: a) when a new species is both morphologically and molecularly distinct from other known species; b) when a new species and closely related species are morphologically indistinguishable, but genetically distinct; and c) how to handle potentially cryptic species and cases where morphotypes are clearly distinct but have the same rDNA sequence. The protocol also addresses other molecular, morphological, and genetic approaches required to resolve species boundaries in the small minority of species where the D1-D3/ITS region phylogenies fail.

Genetic Variability of the Mating Recognition Gene in Populations of Brachionus plicatilis

The development of reproductive barriers promotes within-species divergence and is a requisite for speciation to occur. Mate recognition in the rotifer B. plicatilis is mediated through a surface glycoprotein called Mating Recognition Protein (MRP). Here we investigate the genetic variation of the mmr-b, MRP coding, gene in different natural populations of B. plicatilis from the Iberian Peninsula, that present different degree of population differentiation, with known adaptive divergence in some cases. The MRP gene consists of several nearly identical tandem repeats. We found a relatively high diversity within and among populations both in the number of repeats, as well as in the nucleotide sequence. Despite that most changes are neutral, variation that can potentially affect the protein function was found in two polymorphic sites within a repeat in some of these populations. Although being mostly subject to stabilizing selection, we have found a noticeable pattern of increasing mmr-b gene diversification correlated to increasing differences in environmental factors. The interplay between genetic differentiation, local adaptation and differentiation of the mating recognition system can lead to speciation events in nearly sympatric populations.

Reproductive character displacement allows two sexually deceptive orchids to coexist and attract the same specific pollinator

An increased divergence in characters between species in secondary contact can be shaped by selection against competition for a common resource (ecological character displacement, ECD) or against maladapted hybridization (reproductive character displacement, RCD). These selective pressures can act between incipient species (reinforcement) or well-separated species that already completed the speciation process, but that can still hybridize and produce maladapted hybrids. Here, we investigated two well-separated sexually deceptive orchid species that, unusually, share their specific pollinator. Sympatric individuals of these species are more divergent than allopatric ones in floral characters involved in a mechanical isolating barrier, a pattern suggestive of RCD. To experimentally test this scenario, we built an artificial sympatric population with allopatric individuals. We measured flower characters, genotyped the offspring in natural and artificial sympatry and estimated fertility of hybrids. Different from naturally sympatric individuals, allopatric individuals in artificial sympatry hybridized widely. Hybrids showed lower pollination success and seed viability than parentals. Character displacement did not affect plant pollination success. These findings suggest that RCD evolved between these species to avoid hybridization and that selection on reinforcement may be very strong even in plants with highly specialized pollination.

Comparative phylogeography among eight Neotropical wild cat species: no single evolutionary pattern

Abstract The felid species of South America are thought to have arrived on the continent during the Great American Biotic Interchange (GABI) in the Pleistocene. However, molecular and palaeontological data do not agree on how this event affected speciation in felids. Here, we determine both the number of colonization events and the period when felines first migrated from North America to South America. In addition, we evaluate whether similar evolutionary events could have affected the eight Neotropical cat species in their levels of genetic diversity, spatial genetic structure and demographic changes. We analysed four concatenated mitochondrial genes of the jaguar, ocelot, margay, tigrina, pampas cat, Andean cat, puma and jaguarundi. The samples were representative of a wide distribution of these species in Central and South America. Our analysis suggests either three or four colonization events from North America to South America over the past 3 Myr, followed by subsequent speciation events and the attainment of high or very high genetic diversity levels for seven of the species. No unique evolutionary process was detected for any of the current Neotropical cat species.

The roles of recombination and selection in shaping genomic divergence in an incipient ecological species complex.

Speciation genomic studies have revealed that genomes of diverging lineages are shaped jointly by the actions of gene flow and selection. These evolutionary forces acting in concert with processes such as recombination and genome features such as gene density shape a mosaic landscape of divergence. We investigated the roles of recombination and gene density in shaping the patterns of differentiation and divergence between the cyclically parthenogenetic ecological sister-taxa, Daphnia pulicaria and Daphnia pulex. First, we assembled a phased chromosome-scale genome assembly using trio-binning for D. pulicaria and constructed a genetic map using an F2-intercross panel to understand sex-specific recombination rate heterogeneity. Finally, we used a ddRADseq data set with broad geographic sampling of D. pulicaria, D. pulex, and their hybrids to understand the patterns of genome-scale divergence and demographic parameters. Our study provides the first sex-specific estimates of recombination rates for a cyclical parthenogen, and unlike other eukaryotic species, we observed male-biased heterochiasmy in D. pulicaria, which may be related to this somewhat unique breeding mode. Additionally, regions of high gene density and recombination are generally more divergent than regions of suppressed recombination. Outlier analysis indicated that divergent genomic regions are probably driven by selection on D. pulicaria, the derived lineage colonizing a novel lake habitat. Together, our study supports a scenario of selection acting on genes related to local adaptation shaping genome-wide patterns of differentiation despite high local recombination rates in this species complex. Finally, we discuss the limitations of our data in light of demographic uncertainty.

Detection and diversity of the mannosylerythritol lipid (MEL) gene cluster and lipase A and B genes of Moesziomyces antarcticus isolated from terrestrial sites chronically contaminated with crude oil in Trinidad

BackgroundMannosylerythritol lipids (MELs) belong to the class of glycolipid biosurfactants and are produced by members of the Ustilago and Moesziomyces genera. Production of MELs is regulated by a biosynthetic gene cluster (MEL BGC). Extracellular lipase activity is also associated with MEL production. Most microbial glycolipid-producers are isolated from oil-contaminated environments. MEL-producing yeast that are capable of metabolizing crude oil are understudied, and there is very limited data on indigenous strains from tropical climates. Analysis of the MEL BGC and lipase genes in Trinidad M. antarcticus strains, using a gene-targeted approach, revealed a correlation between their intrinsic capability to degrade crude oil and their adaptation to survive in a chronically polluted terrestrial environment.ResultsM. antarcticus was isolated from naturally-occurring crude oil seeps and an asphaltic mud volcano in Trinidad; these are habitats that have not been previously reported for this species. Genus identification was confirmed by the large-subunit (LSU) and the small-subunit (SSU) sequence comparisons and species identification was confirmed by ITS sequence comparisons and phylogenetic inference. The essential genes (Emt1, Mac1, Mac2, Mmf1) of the MEL BGC were detected with gene-specific primers. Emt1p, Mac1p and Mmf1p sequence analyses confirmed that the Trinidad strains harboured novel synonymous amino acid (aa) substitutions and structural comparisons revealed different regions of disorder, specifically for the Emt1p sequence. Functionality of each protein sequence was confirmed through motif mining and mutation prediction. Phylogenetic relatedness was inferred for Emt1p, Mac1p and Mmf1p sequences. The Trinidad strains clustered with other M. antarcticus sequences, however, the representative Trinidad M. antarcticus sequences consistently formed a separate, highly supported branch for each protein. Similar phylogenetic placement was indicated for LipA and LipB nucleotide and protein sequences. The Trinidad strains also demonstrated lipolytic activity in culture, with an ability to utilize different carbon sources. Comparative evolution of MEL BGC and LipA gene suggested early and late duplication events, depending on the gene, followed by a number of speciation events within Ustilaginaceae. M. antarcticus and M. aphidis were separated from all other members of Ustilaginaceae and two gene homologues were detected, one for each species.ConclusionsSequence analyses was based on a novel gene-targeted approach to analyze the essential genes of the MEL BGC and LipA and LipB genes of M. antarcticus strains from Trinidad. The findings indicated that these strains accumulated nucleotide mutations to a threshold level that did not affect the function of specific proteins encoded by the MEL BGC and LipA and LipB genes. The biosurfactant and lipase enzymes secreted by these Trinidad M. antarcticus strains facilitated their survival in oil-contaminated terrestrial environments. These findings suggest that the Trinidad strains should be explored as promising candidates for the commercial production of MEL biosurfactants and lipase enzymes.

Shifting balances in the weighting of sensory modalities are predicted by divergence in brain morphology in incipient species of Heliconius butterflies

Integrating and weighting sensory perception across modalities is crucial to how animals adapt to their environment. Divergence in brain structure is often in sensory processing regions, suggesting that investment reflects ecological needs. Here, we use two parapatric closely related species, Heliconius erato cyrbia and Heliconius himera, to test the hypothesis that divergence in sensory brain regions affects foraging decisions. These butterflies are isolated across an ecological gradient, which is linked to differences in brain morphology, with H. e. cyrbia investing more in visual centres and H. himera investing in olfactory centres. Here, we demonstrate that these two species vary in how they associate visual and olfactory cues with positive food rewards. We found that when individuals were trained on paired olfactory and visual stimuli, then presented with these stimuli in conflict, they showed distinct behavioural responses. Heliconius himera was more likely to favour positive olfactory cues than H. e. cyrbia, which favoured visual cues regardless of the paired stimulus. This suggests that these species have diverged in the emphasis placed on these different sensory domains during foraging, consistent with observed differences in brain morphology. This result strengthens evidence that speciation initiated by local adaptation is partly facilitated by changes in the neural basis of key behavioural functions.