BMC Evolutionary Biology

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August 29, 2014

06:00
Background: Lysozyme g is an antibacterial enzyme that was first found in the eggs of some birds, but recently has been found in additional species, including non-vertebrates. Some previously characterized lysozyme g sequences are suggested to have altered secretion potential and enzymatic activity, however the distribution of these altered sequences is unknown. Duplicated copies of the lysozyme g gene exist in some species; however, the origins of the duplicates and their roles in altered function are unclear. Results: We identified 234 lysozyme g sequences from 118 vertebrate species, including 181 sequences that are full or near full length representing all vertebrate classes except cartilaginous fish. Phylogenetic analysis shows that most lysozyme g gene duplicates are recent or lineage specific events, however three amplification events are more ancient, those in an early amniote, an early mammal, and an early teleost. The older gene duplications are associated with changes in function, including changes in secretion potential and muramidase antibacterial enzymatic activity. Conclusions: Lysozyme g is an essential muramidase enzyme that is widespread in vertebrates. Duplication of the lysozyme g gene, and the retention of non-secreted isozymes that have lost enzymatic activity indicate that lysozyme g has an activity other than the muramidase activity associated with being an antibacterial enzyme.

August 28, 2014

18:00
Background: A compelling demonstration of adaptation by natural selection is the ability of parasites to manipulate host behavior. One dramatic example involves fungal species from the genus Ophiocordyceps that control their ant hosts by inducing a biting behavior. Intensive sampling across the globe of ants that died after being manipulated by Ophiocordyceps suggests that this phenomenon is highly species-specific. We advance our understanding of this system by reconstructing host manipulation by Ophiocordyceps parasites under controlled laboratory conditions and combining this with field observations of infection rates and a metabolomics survey. Results: We report on a newly discovered species of Ophiocordyceps unilateralis sensu lato from North America that we use to address the species-specificity of Ophiocordyceps-induced manipulation of ant behavior. We show that the fungus can kill all ant species tested, but only manipulates the behavior of those it infects in nature. To investigate if this could be explained at the molecular level, we used ex vivo culturing assays to measure the metabolites that are secreted by the fungus to mediate fungus-ant tissue interactions. We show the fungus reacts heterogeneously to brains of different ant species by secreting a different array of metabolites. By determining which ion peaks are significantly enriched when the fungus is grown alongside brains of its naturally occurring host, we discovered candidate compounds that could be involved in behavioral manipulation by O. unilateralis s.l.. Two of these candidates are known to be involved in neurological diseases and cancer. Conclusions: The integrative work presented here shows that ant brain manipulation by O. unilateralis s.l. is species-specific seemingly because the fungus produces a specific array of compounds as a reaction to the presence of the host brain it has evolved to manipulate. These studies have resulted in the discovery of candidate compounds involved in establishing behavioral manipulation by this specialized fungus and therefore represent a major advancement towards an understanding of the molecular mechanisms underlying this phenomenon.

August 27, 2014

18:00
Background: Myzostomids are marine annelids, nearly all of which live symbiotically on or inside echinoderms, chiefly crinoids, and to a lesser extent asteroids and ophiuroids. These symbionts possess a variety of adult body plans and lifestyles. Most described species live freely on the exterior of their hosts as adults (though starting life on the host inside cysts), while other taxa permanently reside in galls, cysts, or within the host?s mouth, digestive system, coelom, or gonads. Myzostomid lifestyles range from stealing incoming food from the host?s food grooves to consuming the host?s tissue directly. Previous molecular studies of myzostomids have had limited sampling with respect to assessing the evolutionary relationships within the group; therefore molecular data from 75 myzostomid taxa were analyzed using maximum likelihood and maximum parsimony methods. To compare relationships of myzostomids with their hosts, a phylogeny was inferred for 53 hosts and a tanglegram constructed with 88 associations. Results: Gall- and some cyst-dwellers were recovered as a clade, while cyst-to-free-living forms were found as a grade including two clades of internal host-eaters (one infecting crinoids and the other asteroids and ophiuroids), mouth/digestive system inhabitants, and other cyst-dwellers. Clades of myzostomids were recovered that associated with asteroids, ophiuroids, and stalked or feather star crinoids. Co-phylogenetic analyses rejected a null-hypothesis of random associations at the global level, but not for individual associations. Event-based analyses relied most upon host-switching and duplication events to reconcile the association history. Conclusion: Hypotheses were revised concerning the systematics and evolution of Myzostomida, as well their relationships to their hosts. We found two or three transitions between food-stealing and host-eating. Taxa that dwell within the mouth or digestive system and some cyst forms are arguably derived from cyst-to-free-living ancestors ? possibly the result of a free-living form moving to the mouth and paedomorphic retention of the juvenile cyst. Phylogenetic conservatism in host use was observed among related myzostomid taxa. This finding suggests that myzostomids (which have a free-living planktonic stage) are limited to one or a few closely related hosts, despite most hosts co-occurring on the same reefs, many within physical contact of each other.
06:00
Background: Drosophila Dscam1 is a cell-surface protein that plays important roles in neural development and axon tiling of neurons. It is known that thousands of isoforms bind themselves through specific homophilic interactions, a process which provides the basis for cellular self-recognition. Detailed biochemical studies of specific isoforms strongly suggest that homophilic binding, i.e. the formation of homodimers by identical Dscam1 isomers, is of great importance for the self-avoidance of neurons. Due to experimental limitations, it is currently impossible to measure the homophilic binding affinities for all 19,000 potential isoforms. Results: Here we reconstructed the DNA sequences of an ancestral Dscam form (which likely existed approximately 40?~?50 million years ago) using a comparative genomic approach. On the basis of this sequence, we established a working model to predict the self-binding affinities of all isoforms in both the current and the ancestral genome, using machine-learning methods. Detailed computational analysis was performed to compare the self-binding affinities of all isoforms present in these two genomes. Our results revealed that 1) isoforms containing newly derived variable domains exhibit higher self-binding affinities than those with conserved domains, and 2) current isoforms display higher self-binding affinities than their counterparts in the ancient genome. As thousands of Dscam isoforms are needed for the self-avoidance of the neuron, we propose that an increase in self-binding affinity provides the basis for the successful evolution of the arthropod brain. Conclusions: Our data presented here provide an excellent model for future experimental studies of the binding behavior of Dscam isoforms. The results of our analysis indicate that evolution favored the rise of novel variable domains thanks to their higher self-binding affinities, rather than selection merely on the basis of simple expansion of isoform diversity, as that this particular selection process would have established the powerful mechanisms required for neuronal self-avoidance. Thus, we reveal here a new molecular mechanism for the successful evolution of arthropod brains.
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Background: Fleas, the most notorious insect ectoparasites of human, dogs, cats, birds, etc., have recently been traced to its basal and primitive ancestors during the Middle Jurassic. Compared with extant fleas, these large basal fleas have many different features. Although several fossil species with transitional morphologies filled the evolutionary blank, the early evolution of these ectoparasites is still poorly known. Results: Here we report a new flea with transitional characters, Pseudopulex tanlan sp. nov., assigned to Pseudopulicidae, from the Lower Cretaceous Yixian Formation of Liaoning Province, China. Different from the previously described pseudopulicids, P. tanlan has relatively smaller body size but lacking any ctenidia on the tibiae or body, while the male with comparatively smaller and shorter genitalia. On the other hand, P. tanlan has some characters similar to the transitional fleas of saurophthirids, such as, a small head, short compacted antennae, small pygidium and many stiff setae covering the body. Conclusions: Even though other possibilities can not be ruled out, the female specimen with extremely distended abdomen suggests that it might have consumed its last meal before its demise. Compared with other reported female flea fossils, we calculate and estimate that P. tanlan sp. nov. might have consumed 0.02 milliliter (ml) of blood, which is about 15 times of the intake volume by extant fleas. These new findings further support that fleas had evolved a broad diversity by the Early Cretaceous.

August 23, 2014

06:00
Background: Branched polymers of glucose are universally used for energy storage in cells, taking the form of glycogen in animals, fungi, Bacteria, and Archaea, and of amylopectin in plants. Some enzymes involved in glycogen and amylopectin metabolism are similarly conserved in all forms of life, but some, interestingly, are not. In this paper we focus on the phylogeny of glycogen branching and debranching enzymes, respectively involved in introducing and removing of the ?(1?6) bonds in glucose polymers, bonds that provide the unique branching structure to glucose polymers. Results: We performed a large-scale phylogenomic analysis of branching and debranching enzymes in over 400 completely sequenced genomes, including more than 200 from eukaryotes. We show that branching and debranching enzymes can be found in all kingdoms of life, including all major groups of eukaryotes, and thus were likely to have been present in the last universal common ancestor (LUCA) but have been lost in seemingly random fashion in numerous single-celled eukaryotes. We also show how animal branching and debranching enzymes evolved from their LUCA ancestors by acquiring additional domains. Furthermore, we show that enzymes commonly perceived as orthologous, such as human branching enzyme GBE1 and E. coli branching enzyme GlgB, are in fact related by a gene duplication and consequently paralogous. Conclusions: Despite being usually associated with animal liver glycogen and plant starch, energy storage in the form of branched glucose polymers is clearly an ancient process and has probably been present in the last universal common ancestor of all present life. The evolution of the enzymes enabling this form of energy storage is more complex than previously thought and illustrates the need for explicit phylogenomic analysis in the study of even seemingly ?simple? metabolic enzymes. Patterns of conservation in the evolution of the glycogen/starch branching and debranching enzymes hint at some as yet unknown mechanisms, as mutations disrupting these patterns lead to a variety of genetic diseases in humans and other mammals.

August 22, 2014

06:00
Background: Vertebrate mitogenomes are economically organized and usually lack intergenic sequences other than the control region. Intergenic spacers located between the tRNAThr and tRNAPro genes (?T-P spacers?) have been observed in several taxa, including gadiform species, but information about their biological roles and putative functions is still lacking. Results: Sequence characterization of the complete European hake Merluccius merluccius mitogenome identified a complex T-P spacer ranging in size from 223?532?bp. Further analyses of 32 gadiform species, representing 8 families and 28 genera, revealed the evolutionary preserved presence of T-P spacers across all taxa. Molecular complexity of the T-P spacers was found to be coherent with the phylogenetic relationships, supporting a common ancestral origin and gain of function during codfish evolution. Intraspecific variation of T-P spacer sequences was assessed in 225 Atlantic cod specimens and revealed 26 haplotypes. Pyrosequencing data representing the mito-transcriptome poly (A) fraction in Atlantic cod identified an abundant H-strand specific long noncoding RNA of about 375?nt. The T-P spacer corresponded to the 5? part of this transcript, which terminated within the control region in a tail-to-tail configuration with the L-strand specific transcript (the 7S RNA). Conclusions: The T-P spacer is inferred to be evolutionary preserved in gadiform mitogenomes due to gain of function through a long noncoding RNA. We suggest that the T-P spacer adds stability to the H-strand specific long noncoding RNA by forming stable hairpin structures and additional protein binding sites.

August 21, 2014

18:00
Background: Thylacocephala is a group of enigmatic extinct arthropods. Here we provide a full description of the oldest unequivocal thylacocephalan, a new genus and species Thylacares brandonensis, which is present in the Silurian Waukesha fauna from Wisconsin, USA. We also present details of younger, Jurassic specimens, from the Solnhofen lithographic limestones, which are crucial to our interpretation of the systematic position of Thylacocephala. In the past, Thylacocephala has been interpreted as a crustacean ingroup and as closely related to various groups such as cirripeds, decapods or remipeds. Results: The Waukesha thylacocephalan, Thylacares brandonensis n. gen. n. sp., bears compound eyes and raptorial appendages that are relatively small compared to those of other representatives of the group. As in other thylacocephalans the large bivalved shield encloses much of the entire body. The shield lacks a marked optical notch. The eyes, which project just beyond the shield margin, appear to be stalked. Head appendages, which may represent antennulae, antennae and mandibles, appear to be present. The trunk is comprised of up to 22 segments. New details observed on thylacocephalans from the Jurassic Solnhofen lithographic limestones include antennulae and antennae of Mayrocaris bucculata, and endites on the raptorial appendages and an elongate last trunk appendage in Clausocaris lithographica. Preserved features of the internal morphology in C. lithographica include the muscles of the raptorial appendage and trunk. Conclusions: Our results indicate that some ‘typical’ thylacocephalan characters are unique to the group; these autapomorphies contribute to the difficulty of determining thylacocephalan affinities. While the new features reported here are consistent with a eucrustacean affinity, most previous hypotheses for the position of Thylacocephala within Eucrustacea (as Stomatopoda, Thecostraca or Decapoda) are shown to be unlikely. A sister group relationship to Remipedia appears compatible with the observed features of Thylacocephala but more fossil evidence is required to test this assertion. The raptorial appendages of Thylacocephala most likely projected 45 degrees abaxially instead of directly forward as previously reconstructed. The overall morphology of thylacocephalans supports a predatory mode of life.

August 17, 2014

06:00
Background: Specific host-parasite systems often embody a particular co-distribution phenomenon, in which the parasite’s phylogeographic pattern is dependent on its host. In practice, however, both congruent and incongruent phylogeographic patterns between the host and the parasite have been reported. Here, we compared the population genetics of the plateau zokor (Eospalax baileyi), a subterranean rodent, and its host-associated flea species, Neopsylla paranoma, with an aim to determine whether the two animals share a similar phylogeographic pattern. Results: We sampled 130 host-parasite pairs from 17 localities in the Qinghai-Tibet Plateau (QTP), China, and sequenced a mitochondrial DNA (mtDNA) segment (~2,500 bp), including the complete COI and COII genes. We also detected 55 zokor and 75 flea haplotypes. AMOVA showed that the percentage of variation among the populations of zokors constituted 97.10%, while the within population variation was only 2.90%; for fleas, the values were 85.68% and 14.32%, respectively. Moreover, the flea Fst (fixation index) values were significantly smaller than in zokor. Although the Fst values between zokors and fleas were significantly and positively correlated (N =105, R =0.439, p =0.000), only a small amount (R 2 = 0.19) of the flea Fst variations could be explained by the zokor Fst variations. The two animals showed very distinct haplotype network structures from each other while co-phylogenetic analyses were unable to reject the hypothesis of an independence of speciation events. Conclusions: Zokors and fleas have very distinct population genetic patterns from each other, likely due to the influence of other sympatrically-distributed vertebrates on the transmission of fleas.

August 15, 2014

06:00
Background: Social information use is usually considered to lead to ecological convergence among involved con- or heterospecific individuals. However, recent results demonstrate that observers can also actively avoid behaving as those individuals being observed, leading to ecological divergence. This phenomenon has been little explored so far, yet it can have significant impact on resource use, realized niches and species co-existence. In particular, the time-scale and the ecological context over which such shifts can occur are unknown. We examined with a long-term (four years) field experiment whether experimentally manipulated, species-specific, nest-site feature preferences (symbols on nest boxes) are transmitted across breeding seasons and affect future nest-site preferences in a guild of three cavity-nesting birds. Results: Of the examined species, resident great tits (Parus major) preferred the symbol that had been associated with unoccupied nest boxes in the previous year, i.e., their preference shifted towards niche space previously unused by putative competitors and conspecifics. Conclusions: Our results show that animals can remember the earlier resource use of conspecifics and other guild members and adjust own decisions accordingly one year after. Our experiment cannot reveal the ultimate mechanism(s) behind the observed behaviour but avoiding costs of intra- or interspecific competition or ectoparasite load in old nests are plausible reasons. Our findings imply that interspecific social information use can affect resource sharing and realized niches in ecological time-scale through active avoidance of observed decisions and behavior of potentially competing species.

August 13, 2014

18:00
Background: In insect societies, intracolonial genetic variation is predicted to affect both colony efficiency and reproductive skew. However, because the effects of genetic variation on these two colony characteristics have been tested independently, it remains unclear whether they are affected by genetic variation independently or in a related manner. Here we test the effect of genetic variation on colony efficiency and reproductive skew in a rhinotermitid termite, Reticulitermes speratus, a species in which female-female pairs can facultatively found colonies. We established colonies using two types of female-female pairs: colonies founded by sisters (i.e., sister-pair colonies) and those founded by females from different colonies (i.e., unrelated-pair colonies). Colony growth and reproductive skew were then compared between the two types of incipient colonies. Results: At 15 months after colony foundation, unrelated-pair colonies were larger than sister-pair colonies, although the caste ratio between workers and nymphs, which were alternatively differentiated from young larvae, did not differ significantly. Microsatellite DNA analyses of both founders and their parthenogenetically produced offspring indicated that, in both sister-pair and unrelated-pair colonies, there was no significant skew in the production of eggs, larvae, workers and soldiers. Nymph production, however, was significantly more skewed in the sister-pair colonies than in unrelated-pair colonies. Because nymphs can develop into winged adults (alates) or nymphoid reproductives, they have a higher chance of direct reproduction than workers in this species. Conclusions: Our results support the idea that higher genetic variation among colony members could provide an increase in colony productivity, as shown in hymenopteran social insects. Moreover, this study suggests that low genetic variation (high relatedness) between founding females increases reproductive skew via one female preferentially channeling her relatives along the reproductive track. This study thus demonstrated that, in social insects, intracolonial genetic variation can simultaneously affect both colony efficiency and reproductive skew.
18:00
Background: Gene flow plays an important role in domestication history of domesticated species. However, little is known about the demographic history of domesticated silkworm involving gene flow with its wild relative. Results: In this study, four model-based evolutionary scenarios to describe the demographic history of B. mori were hypothesized. Using Approximate Bayesian Computation method and DNA sequence data from 29 nuclear loci, we found that the gene flow at bottleneck model is the most likely scenario for silkworm domestication. The starting time of silkworm domestication was estimated to be approximate 7,500 years ago; the time of domestication termination was 3,984 years ago. Using coalescent simulation analysis, we also found that bi-directional gene flow occurred during silkworm domestication. Conclusions: Estimates of silkworm domestication time are nearly consistent with the archeological evidence and our previous results. Importantly, we found that the bi-directional gene flow might occur during silkworm domestication. Our findings add a dimension to highlight the important role of gene flow in domestication of crops and animals.

August 12, 2014

18:00
Background: Pigmentation has a long history of investigation in evolutionary biology. In Drosophila melanogaster, latitudinal and altitudinal clines have been found but their underlying causes remain unclear. Moreover, most studies were conducted on cosmopolitan populations which have a relatively low level of genetic structure and diversity compared to sub-Saharan African populations. We investigated: 1) the correlation between pigmentation traits within and between the thorax and the fourth abdominal segment, and 2) their associations with different geographical and ecological variables, using 710 lines belonging to 30 sub-Saharan and cosmopolitan populations. Results: Pigmentation clines substantially differed between sub-Saharan and cosmopolitan populations. While positive correlations with latitude have previously been described in Europe, India and Australia, in agreement with Bogert's rule or the thermal melanism hypothesis, we found a significant negative correlation in Africa. This correlation persisted even after correction for altitude, which in its turn showed a positive correlation with pigmentation independently from latitude. More importantly, we found that thoracic pigmentation reaches its maximal values in this species in high-altitude populations of Ethiopia (1,600-3,100 m). Ethiopian flies have a diffuse wide thoracic trident making the mesonotum and the head almost black, a phenotype that is absent from all other sub-Saharan or cosmopolitan populations including high-altitude flies from Peru (~3,400 m). Ecological analyses indicated that the variable most predictive of pigmentation in Africa, especially for the thorax, was ultra-violet (UV) intensity, consistent with the so-called Gloger's rule invoking a role of melanin in UV protection. Conclusion: Our data suggest that different environmental factors may shape clinal variation in tropical and temperate regions, and may lead to the evolution of different degrees of melanism in different high altitude populations in the tropics.
06:00
Background: Aquaporins (AQPs) and aquaglyceroporins (AQGPs) belong to the superfamily of Major Intrinsic Proteins (MIPs) and are involved in the transport of water and neutral solutes across the membranes. MIP channels play significant role in plant-fungi symbiotic relationship and are believed to be important in host-pathogen interactions in human fungal diseases. In plants, at least five major MIP subfamilies have been identified. Fungal MIP subfamilies include orthodox aquaporins and five subgroups within aquaglyceroporins. XIP subfamily is common to both plants and fungi. In this study, we have investigated the extent of diversity in fungal MIPs and explored further evolutionary relationships with the plant MIP counterparts. Results: We have extensively analyzed the available fungal genomes and examined nearly 400 fungal MIPs. Phylogenetic analysis and homology modeling exhibit the existence of a new MIP cluster distinct from any of the known fungal MIP subfamilies. All members of this cluster are found in microsporidia which are unicellular fungal parasites. Members of this family are small in size, charged and have hydrophobic residues in the aromatic/arginine selectivity filter and these features are shared by small and basic intrinsic proteins (SIPs), one of the plant MIP subfamilies. We have also found two new subfamilies (δ and γ2) within the AQGP group. Fungal AQGPs are the most diverse and possess the largest number of subgroups. We have also identified distinguishing features in loops E and D in the newly identified subfamilies indicating their possible role in channel transport and gating. Conclusions: Fungal SIP-like MIP family is distinct from any of the known fungal MIP families including orthodox aquaporins and aquaglyceroporins. After XIPs, this is the second MIP subfamily from fungi that may have possible evolutionary link with a plant MIP subfamily. AQGPs in fungi are more diverse and possess the largest number of subgroups. The aromatic/arginine selectivity filter of SIP-like fungal MIPs and the δ AQGPs are unique, hydrophobic in nature and are likely to transport novel hydrophobic solutes. They can be attractive targets for developing anti-fungal drugs. The evolutionary pattern shared with their plant counterparts indicates possible involvement of new fungal MIPs in plant-fungi symbiosis and host-pathogen interactions.

August 9, 2014

18:00
Background: Given that most species that have ever existed on earth are extinct, it stands to reason that the evolutionary history can be better understood with fossil taxa. Bauhinia is a typical genus of pantropical intercontinental disjunction among the Asian, African, and American continents. Geographic distribution patterns are better recognized when fossil records and molecular sequences are combined in the analyses. Here, we describe a new macrofossil species of Bauhinia from the Upper Miocene Xiaolongtan Formation in Wenshan County, Southeast Yunnan, China, and elucidate the biogeographic significance through the analyses of molecules and fossils. Results: Morphometric analysis demonstrates that the leaf shapes of B. acuminata, B. championii, B. chalcophylla, B. purpurea, and B. podopetala closely resemble the leaf shapes of the new finding fossil. Phylogenetic relationships among the Bauhinia species were reconstructed using maximum parsimony and Bayesian inference, which inferred that species in Bauhinia species are well-resolved into three main groups. Divergence times were estimated by the Bayesian Markov chain Monte Carlo (MCMC) method under a relaxed clock, and inferred that the stem diversification time of Bauhinia was ca. 62.7 Ma. The Asian lineage first diverged at ca. 59.8 Ma, followed by divergence of the Africa lineage starting during the late Eocene, whereas that of the neotropical lineage starting during the middle Miocene. Conclusions: Hypotheses relying on vicariance or continental history to explain pantropical disjunct distributions are dismissed because they require mostly Palaeogene and older tectonic events. We suggest that Bauhinia originated in the middle Paleocene in Laurasia, probably in Asia, implying a possible Tethys Seaway origin or an “Out of Tropical Asia”, and dispersal of legumes. Its present pantropical disjunction resulted from disruption of the boreotropical flora by climatic cooling after the Paleocene-Eocene Thermal Maximum (PETM). North Atlantic land bridges (NALB) seem the most plausible route for migration of Bauhinia from Asia to America; and additional aspects of the Bauhinia species distribution are explained by migration and long distance dispersal (LDD) from Eurasia to the African and American continents.

August 7, 2014

18:00
Background: Discordance among individual molecular age estimates, or between molecular age estimates and the fossil record, is observed in many clades across the Tree of Life. This discordance is attributed to a variety of variables including calibration age uncertainty, calibration placement, nucleotide substitution rate heterogeneity, or the specified molecular clock model. However, the impact of changes in phylogenetic informativeness of individual genes over time on phylogenetic inferences is rarely analyzed. Using nuclear and mitochondrial sequence data for ray-finned fishes (Actinopterygii) as an example, we extend the utility of phylogenetic informativeness profiles to predict the time intervals when nucleotide substitution saturation results in discordance among molecular ages estimated. Results: We demonstrate that even with identical calibration regimes and molecular clock methods, mitochondrial based molecular age estimates are systematically older than those estimated from nuclear sequences. This discordance is most severe for highly nested nodes corresponding to more recent (i.e., Jurassic-Recent) divergences. By removing data deemed saturated, we reconcile the competing age estimates and highlight that the older mtDNA based ages were driven by nucleotide saturation. Conclusions: Homoplasious site patterns in a DNA sequence alignment can systematically bias molecular divergence time estimates. Our study demonstrates that PI profiles can provide a non-arbitrary criterion for data exclusion to mitigate the influence of homoplasy on time calibrated branch length estimates. Analyses of actinopterygian molecular clocks demonstrate that scrutiny of the time scale on which sequence data is informative is a fundamental, but generally overlooked, step in molecular divergence time estimation.

August 6, 2014

06:00
Background: Female mate choice after mating is a strong force in sexual selection and could lead to coevolution of mating traits between the sexes. How females of different genotypes respond to substances in the male ejaculate should be mediated by females’ mate choices. Monoamines regulate animal physiology and behavior, including the post-mating behavior of females of the adzuki bean beetle, Callosobruchus chinensis (Coleoptera: Bruchidae). This study examined differences in females’ response to four monoamines (dopamine, octopamine, tyramine, serotonin) between strains from different populations of C. chinensis. Results: Injection with either octopamine or tyramine, two kinds of monoamines significantly reduced female receptivity in two strains with low remating frequencies. None of the four monoamines reduced female receptivity in one strain with high remating frequencies. However, all monoamines reduced it in another strain with high remating frequencies. Oviposition was activated by tyramine on days 1–5 or by serotonin on days 4 and 5 in the two strains with low remating frequencies, but only on day 1 or day 4 in the strains with high remating frequencies. Conclusion: These differences in female response to monoamines, especially tyramine and serotonin, correspond with results of previous studies. They indicate differences in female response to male substances that reduce receptivity and activate oviposition. These findings suggest relationships between the differences in female response to male substances among populations and mutations in the pathways of monoamine biosynthesis or transmission, which in turn determine female mate choice in response to male substances.

August 5, 2014

18:00
Background: Dacts are multi-domain adaptor proteins. They have been implicated in Wnt and Tgfβ signaling and serve as a nodal point in regulating many cellular activities. Dact genes have so far only been identified in bony vertebrates. Also, the number of Dact genes in a given species, the number and roles of protein motifs and functional domains, and the overlap of gene expression domains are all not clear. To address these problems, we have taken an evolutionary approach, screening for Dact genes in the animal kingdom and establishing their phylogeny and the synteny of Dact loci. Furthermore, we performed a deep analysis of the various Dact protein motifs and compared the expression patterns of different Dacts. Results: Our study identified previously not recognized dact genes and showed that they evolved late in the deuterostome lineage. In gnathostomes, four Dact genes were generated by the two rounds of whole genome duplication in the vertebrate ancestor, with Dact1/3 and Dact2/4, respectively, arising from the two genes generated during the first genome duplication. In actinopterygians, a further dact4r gene arose from retrotranscription. The third genome duplication in the teleost ancestor, and subsequent gene loss in most gnathostome lineages left extant species with a subset of Dact genes. The distribution of functional domains suggests that the ancestral Dact function lied with Wnt signaling, and a role in Tgfβ signaling may have emerged with the Dact2/4 ancestor. Motif reduction, in particular in Dact4, suggests that this protein may counteract the function of the other Dacts. Dact genes were expressed in both distinct and overlapping domains, suggesting possible combinatorial function. Conclusions: The gnathostome Dact gene family comprises four members, derived from a chordate-specific ancestor. The ability to control Wnt signaling seems to be part of the ancestral repertoire of Dact functions, while the ability to inhibit Tgfβ signaling and to carry out specialized, ortholog-specific roles may have evolved later. The complement of Dact genes coexpressed in a tissue provides a complex way to fine-tune Wnt and Tgfβ signaling. Our work provides the basis for future structural and functional studies aimed at unraveling intracellular regulatory networks.

August 2, 2014

06:00
Background: A compelling demonstration of adaptation by natural selection is the ability of parasites to manipulate host behavior. One dramatic example involves fungal species from the genus Ophiocordyceps that control their ant hosts by inducing a biting behavior. Intensive sampling across the globe of ants that died after being manipulated by Ophiocordyceps suggests that this phenomenon is highly species-specific. We advance our understanding of this system by reconstructing host manipulation by Ophiocordyceps parasites under controlled laboratory conditions and combining this with field observations of infection rates and a metabolomics survey. Results: We report on a newly discovered species of Ophiocordyceps unilateralis sensu lato from North America that we use to address the species-specificity of Ophiocordyceps-induced manipulation of ant behavior. We show that the fungus can kill all ant species tested, but only manipulates the behavior of those it infects in nature. To investigate if this could be explained at the molecular level, we used ex vivo culturing assays to measure the metabolites that are secreted by the fungus to mediate fungus-ant tissue interactions. We show the fungus reacts heterogeneously to brains of different ant species by secreting a different array of metabolites. By determining which ion peaks are significantly enriched when the fungus is grown alongside brains of its naturally occurring host, we discovered candidate compounds that could be involved in behavioral manipulation by O. unilateralis s.l.. Two of these candidates are known to be involved in neurological diseases and cancer. Conclusions: The integrative work presented here shows that ant brain manipulation by O. unilateralis s.l. is species-specific seemingly because the fungus produces a specific array of compounds as a reaction to the presence of the host brain it has evolved to manipulate. These studies have resulted in the discovery of candidate compounds involved in establishing behavioral manipulation by this specialized fungus and therefore represent a major advancement towards an understanding of the molecular mechanisms underlying this phenomenon.

July 31, 2014

04:47
Background: The phylogenetic history of genes underlying phenotypic diversity can offer insight into the evolutionary origin of adaptive traits. This is especially true where single genes have large phenotypic effects, for example in determining polymorphic mimicry in butterflies. Here, we characterise the evolutionary history of two candidate genes for the mimicry switch in the polymorphic Batesian mimic Papilio dardanus coding for the transcription factors engrailed and invected. Results: We show that phased haplotypes associated with the dominant morphs f. poultoni and f. planemoides are phylogenetically highly divergent, in particular at non-synonymous sites. Some non-synonymous changes are shared between the divergent alleles suggesting either convergence or a shared ancestry. Gene trees for invected do not show this pattern. Despite their great divergence, all engrailed alleles of P. dardanus were monophyletic with respect to alleles of closely related species. Phylogenetic analyses therefore reveal no evidence for introgression from other species. A McDonald-Kreitman test conducted on a population sample from South Africa confirms a significant excess of intraspecific non-synonymous diversity in P. dardanus engrailed, suggesting long-term balanced polymorphism at this locus. Conclusions: The divergence between engrailed haplotypes suggests an evolutionary history distorted by selection with multiple changes reflecting recurrent selective sweeps. The high level of intraspecific polymorphism observed is characteristic of balancing selection on this locus, as expected if the gene engrailed is under phenotypic selection for the maintenance of multiple mimetic morphs. Non-synonymous changes in key functional portions of a major transcription factor are likely to be deleterious but if maintained in a dominant allele at low frequency, heterozygosity would reduce the associated genetic load.