Evolution of olfaction in non-avian theropod dinosaurs and birds

Little is known about the olfactory capabilities of extinct basal (non-neornithine) birds or the evolutionary changes in olfaction that occurred from non-avian theropods through modern birds. Although modern birds are known to have diverse olfactory capabilities, olfaction is generally considered to have declined during avian evolution as visual and vestibular sensory enhancements occurred in association with flight. To test the hypothesis that olfaction diminished through avian evolution, we assessed relative olfactory bulb size, here used as a neuroanatomical proxy for olfactory capabilities, in 157 species of non-avian theropods, fossil birds and living birds. We show that relative olfactory bulb size increased during non-avian maniraptoriform evolution, remained stable across the non-avian theropod/bird transition, and increased during basal bird and early neornithine evolution. From early neornithines through a major part of neornithine evolution, the relative size of the olfactory bulbs remained stable before decreasing in derived neoavian clades. Our results show that, rather than decreasing, the importance of olfaction actually increased during early bird evolution, representing a previously unrecognized sensory enhancement. The relatively larger olfactory bulbs of earliest neornithines, compared with those of basal birds, may have endowed neornithines with improved olfaction for more effective foraging or navigation skills, which in turn may have been a factor allowing them to survive the end-Cretaceous mass extinction.     

Multi‐gene phylogeny of jacks and pompanos (Carangidae), including placement of monotypic vadigo Campogramma glaycos

In this study, the phylogenetic trees of jacks and pompanos (Carangidae), an ecologically and morphologically diverse, globally distributed fish family, are inferred from a complete, concatenated data set of two mitochondrial (cytochrome c oxidase I, cytochrome b) loci and one nuclear (myosin heavy chain 6) locus. Maximum likelihood and Bayesian inferences are largely congruent and show a clear separation of Carangidae into the four subfamilies: Scomberoidinae, Trachinotinae, Naucratinae and Caranginae. The inclusion of the carangid sister lineages Coryphaenidae (dolphinfishes) and Rachycentridae (cobia), however, render Carangidae paraphyletic. The phylogenetic trees also show with high statistical support that the monotypic vadigo Campogramma glaycos is the sister to all other species within the Naucratinae.     

A molecular approach to the phylogenetic relationships of the western palaearctic Helicoidea (Gastropoda: Stylommatophora)

Molecular phylogenetic relationships among 45 members of the Helicoidea (Gastropoda: Stylommatophora) were examined using partial mitochondrial 16S rRNA sequences. Phylogenetic relationships were inferred using maximum parsimony, maximum likelihood and Bayesian methods. The reconstructed phylogenies showed a good degree of support for more recent branches, but gave little support to deeper nodes. Mitochondrial rDNA data further confirmed monophyletic status of helicids, recognized monachine hygromiid and bradybaenid clades and resolved a number of relationships in the helicelline hygromiids. With the respect to the latter assemblage, most of the anatomically based groups are confirmed, corroborating the diagnostic value of the dart-sac complex and a close affinity between Ichnusomunda sacchii and species of the genus Cernuella . Nevertheless, some well resolved branches challenge previous systematic arrangements, grouping species previously placed in different arrangements. In particular, support was not found for the monophyly of helicelline hygromiids with pedal penial innervation. Possible explanations for these incongruencies are suggested. 16S sequence data are appropriate for studies of relationships within the different species groups and less so for recovery of more ancient radiations in the Helicoidea. It will be valuable to combine the 16S data with other gene sequences to estimate basal relationships.  © 2005 The Linnean Society of London, Biological Journal of the Linnean Society , 2005, 85 , 501–512.     

A new North American therizinosaurid and the role of herbivory in ‘predatory’ dinosaur evolution

Historically, ecomorphological inferences regarding theropod (i.e. ‘predatory’) dinosaurs were guided by an assumption that they were singularly hypercarnivorous. A recent plethora of maniraptoran discoveries has produced evidence challenging this notion. Here, we report on a new species of maniraptoran theropod, Nothronychus graffami sp. nov. Relative completeness of this specimen permits a phylogenetic reassessment of Therizinosauria—the theropod clade exhibiting the most substantial anatomical evidence of herbivory. In the most comprehensive phylogenetic study of the clade conducted to date, we recover Therizinosauria as the basalmost maniraptoran lineage. Using concentrated changes tests, we present evidence for correlated character evolution among herbivorous and hypercarnivorous taxa and propose ecomorphological indicators for future interpretations of diet among maniraptoran clades. Maximum parsimony optimizations of character evolution within our study indicate an ancestral origin for dietary plasticity and facultative herbivory (omnivory) within the clade. These findings suggest that hypercarnivory in paravian dinosaurs is a secondarily derived dietary specialization and provide a potential mechanism for the invasion of novel morpho- and ecospace early in coelurosaurian evolution—the loss of obligate carnivory and origin of dietary opportunism.     

Colonization history of Galapagos giant tortoises: Insights from mitogenomes support the progression rule

Galapagos giant tortoises (Chelonoidis spp.) are a group of large, long-lived reptiles that includes 14 species, 11 of which are extant and threatened by human activities and introductions of non-native species. Here, we evaluated the phylogenetic relationships of all extant and two extinct species (Chelonoidis abingdonii from the island of Pinta and Chelonoidis niger from the island of Floreana) using Bayesian and maximum likelihood analysis of complete or nearly complete mitochondrial genomes. We also provide an updated phylogeographic scenario of their colonization of the Galapagos Islands using chrono-phylogenetic and biogeographic approaches. The resulting phylogenetic trees show three major groups of species: one from the southern, central, and western Galapagos Islands; the second from the northwestern islands; and the third group from the northern, central, and eastern Galapagos Islands. The time-calibrated phylogenetic and ancestral area reconstructions generally align with the geologic ages of the islands. The divergence of the Galapagos giant tortoises from their South American ancestor likely occurred in the upper Miocene. Their diversification on the Galapagos adheres to the island progression rule, starting in the Pleistocene with the dispersal of the ancestral form from the two oldest islands (San Cristóbal and Española) to Santa Cruz, Santiago, and Pinta, followed by multiple colonizations from different sources within the archipelago. Our work provides an example of how to reconstruct the history of endangered taxa in spite of extinctions and human-mediated dispersal events and provides a framework for evaluating the contribution of colonization and in situ speciation to the diversity of other Galapagos lineages.     

Gene-Flow in a Mosaic Hybrid Zone: Is Local Introgression Adaptive?

Genome-wide scans of genetic differentiation between hybridizing taxa can identify genome regions with unusual rates of introgression. Regions of high differentiation might represent barriers to gene flow, while regions of low differentiation might indicate adaptive introgression—the spread of selectively beneficial alleles between reproductively isolated genetic backgrounds. Here we conduct a scan for unusual patterns of differentiation in a mosaic hybrid zone between two mussel species, Mytilus edulis and M. galloprovincialis. One outlying locus, mac-1, showed a characteristic footprint of local introgression, with abnormally high frequency of edulis-derived alleles in a patch of M. galloprovincialis enclosed within the mosaic zone, but low frequencies outside of the zone. Further analysis of DNA sequences showed that almost all of the edulis allelic diversity had introgressed into the M. galloprovincialis background in this patch. We then used a variety of approaches to test the hypothesis that there had been adaptive introgression at mac-1. Simulations and model fitting with maximum-likelihood and approximate Bayesian computation approaches suggested that adaptive introgression could generate a “soft sweep,” which was qualitatively consistent with our data. Although the migration rate required was high, it was compatible with the functioning of an effective barrier to gene flow as revealed by demographic inferences. As such, adaptive introgression could explain both the reduced intraspecific differentiation around mac-1 and the high diversity of introgressed alleles, although a localized change in barrier strength may also be invoked. Together, our results emphasize the need to account for the complex history of secondary contacts in interpreting outlier loci.     

Sensitivity of Ribosomal RNA Character Sampling in the Phylogeny of Rhabditida

Near-full-length 18S and 28S rRNA gene sequences were obtained for 33 nematode species. Datasets were constructed based on secondary structure and progressive multiple alignments, and clades were compared for phylogenies inferred by Bayesian and maximum likelihood methods. Clade comparisons were also made following removal of ambiguously aligned sites as determined using the program ProAlign. Different alignments of these data produced tree topologies that differed, sometimes markedly, when analyzed by the same inference method. With one exception, the same alignment produced an identical tree topology when analyzed by different methods. Removal of ambiguously aligned sites altered the tree topology and also reduced resolution. Nematode clades were sensitive to differences in multiple alignments, and more than doubling the amount of sequence data by addition of 28S rRNA did not fully mitigate this result. Although some individual clades showed substantially higher support when 28S data were combined with 18S data, the combined analysis yielded no statistically significant increases in the number of clades receiving higher support when compared to the 18S data alone. Secondary structure alignment increased accuracy in positional homology assignment and, when used in combination with paired-site substitution models, these structural hypotheses of characters and improved models of character state change yielded high levels of phylogenetic resolution. Phylogenetic results included strong support for inclusion of Daubaylia potomaca within Cephalobidae, whereas the position of Fescia grossa within Tylenchina varied depending on the alignment, and the relationships among Rhabditidae, Diplogastridae, and Bunonematidae were not resolved.     

Dispersal as a means of inbreeding avoidance in a wild bird population

The long-term study of animal populations facilitates detailed analysis of processes otherwise difficult to measure, and whose significance may appear only when a large sample size from many years is available for analysis. For example, inbreeding is a rare event in most natural populations, and therefore many years of data are needed to estimate its effect on fitness. A key behaviour hypothesized to play an important role in avoiding inbreeding is natal dispersal. However, the functional significance of natal dispersal with respect to inbreeding has been much debated but subject to very few empirical tests. We analysed 44 years of data from a wild great tit Parus major population involving over 5000 natal dispersal events within Wytham Woods, UK. Individuals breeding with a relative dispersed over several-fold shorter distances than those outbreeding; within the class of inbreeding birds, increased inbreeding was associated with reduced dispersal distance, for both males and females. This led to a 3.4-fold increase (2.3-5, 95% CI) in the likelihood of close (f=0.25) inbreeding relative to the population average when individuals dispersed less than 200m. In the light of our results, and published evidence showing little support for active inbreeding avoidance in vertebrates, we suggest that dispersal should be considered as a mechanism of prime importance for inbreeding avoidance in wild populations.     

Combining FISH and model-based predictions to understand chromosome evolution in Typhonium (Araceae)

Background and Aims

Since the advent of molecular phylogenetics, numerous attempts have been made to infer the evolutionary trajectories of chromosome numbers on DNA phylogenies. Ideally, such inferences should be evaluated against cytogenetic data. Towards this goal, we carried out phylogenetic modelling of chromosome number change and fluorescence in situ hybridization (FISH) in a medium sized genus of Araceae to elucidate if data from chromosomal markers would support maximum likelihood-inferred changes in chromosome numbers among close relatives. Typhonium, the focal genus, includes species with 2n = 65 and 2n = 8, the lowest known count in the family.

Methods

A phylogeny from nuclear and plastid sequences (96 taxa, 4252 nucleotides) and counts for all included species (15 of them first reported here) were used to model chromosome number evolution, assuming discrete events, such as polyploidization and descending or ascending dysploidy, occurring at different rates. FISH with three probes (5S rDNA, 45S rDNA and Arabidopsis-like telomeres) was performed on ten species with 2n = 8 to 2n = 24.

Key Results

The best-fitting models assume numerous past chromosome number reductions. Of the species analysed with FISH, the two with the lowest chromosome numbers contained interstitial telomeric signals (Its), which together with the phylogeny and modelling indicates decreasing dysploidy as an explanation for the low numbers. A model-inferred polyploidization in another species is matched by an increase in rDNA sites.

Conclusions

The combination of a densely sampled phylogeny, ancestral state modelling and FISH revealed that the species with n = 4 is highly derived, with the FISH data pointing to a Robertsonian fusion-like chromosome rearrangement in the ancestor of this species.     

Temperature-dependent sex-biased embryo mortality in a bird

Sex ratios have important evolutionary consequences and are often biased by environmental factors. The effect of developmental temperature on offspring sex ratios has been widely documented across a diverse range of taxa but has rarely been investigated in birds and mammals. However, recent field observations and artificial incubation experiments have demonstrated that the hatching sex ratio of a megapode, the Australian brush-turkey (Alectura lathami), varied with incubation temperature; more females hatched at high incubation temperatures and more males hatched at low temperatures. Here, we investigated the causes of this temperature-dependent sex-biasing system. Molecular sexing of chicks and embryos confirmed that male embryo mortality was greater at high temperatures while female embryo mortality is greater at low temperatures, with mortality in both sexes similar at intermediate incubation temperatures. Temperature-dependent sex-biased embryo mortality represents a novel mechanism of altering sex ratios in birds. This novel mechanism, coupled with the unique breeding biology of the brush-turkey, offers a potentially unparalleled opportunity in which to investigate sex allocation theory in birds.     

Mobbing calls signal predator category in a kin group-living bird species

Many prey species gather together to approach and harass their predators despite the associated risks. While mobbing, prey usually utter calls and previous experiments have demonstrated that mobbing calls can convey information about risk to conspecifics. However, the risk posed by predators also differs between predator categories. The ability to communicate predator category would be adaptive because it would allow other mobbers to adjust their risk taking. I tested this idea in Siberian jays Perisoreus infaustus, a group-living bird species, by exposing jay groups to mounts of three hawk and three owl species of varying risks. Groups immediately approached to mob the mount and uttered up to 14 different call types. Jays gave more calls when mobbing a more dangerous predator and when in the presence of kin. Five call types were predator-category-specific and jays uttered two hawk-specific and three owl-specific call types. Thus, this is one of the first studies to demonstrate that mobbing calls can simultaneously encode information about both predator category and the risk posed by a predator. Since antipredator calls of Siberian jays are known to specifically aim at reducing the risk to relatives, kin-based sociality could be an important factor in facilitating the evolution of predator-category-specific mobbing calls.     

kakusan: a computer program to automate the selection of a nucleotide substitution model and the configuration of a mixed model on multilocus data

The application of different substitution models to each gene (a.k.a. mixed model) should be considered in model‐based phylogenetic analysis of multigene sequences. However, a single molecular evolution model is still usually applied. There are no computer programs able to conduct model selection for multiple loci at the same time, though several recently developed types of software for phylogenetic inference can handle mixed model. Here, I have developed computer software named ‘kakusan’ that enables us to solve the above problems. Major running steps are briefly described, and an analysis of results with kakusan is compared to that obtained with other program.     

Spatially explicit predictions of blood parasites in a widely distributed African rainforest bird

Critical to the mitigation of parasitic vector-borne diseases is the development of accurate spatial predictions that integrate environmental conditions conducive to pathogen proliferation. Species of Plasmodium and Trypanosoma readily infect humans, and are also common in birds. Here, we develop predictive spatial models for the prevalence of these blood parasites in the olive sunbird (Cyanomitra olivacea). Since this species exhibits high natural parasite prevalence and occupies diverse habitats in tropical Africa, it represents a distinctive ecological model system for studying vector-borne pathogens. We used PCR and microscopy to screen for haematozoa from 28 sites in Central and West Africa. Species distribution models were constructed to associate ground-based and remotely sensed environmental variables with parasite presence. We then used machine-learning algorithm models to identify relationships between parasite prevalence and environmental predictors. Finally, predictive maps were generated by projecting model outputs to geographically unsampled areas. Results indicate that for Plasmodium spp., the maximum temperature of the warmest month was most important in predicting prevalence. For Trypanosoma spp., seasonal canopy moisture variability was the most important predictor. The models presented here visualize gradients of disease prevalence, identify pathogen hotspots and will be instrumental in studying the effects of ecological change on these and other pathogens.     

The enigmatic monotypic crab plover Dromas ardeola is closely related to pratincoles and coursers (Aves, Charadriiformes, Glareolidae)

The phylogenetic placement of the monotypic crab plover Dromasardeola (Aves, Charadriiformes) remains controversial. Phylogenetic analysis of anatomical and behavioral traits using phenetic and cladistic methods of tree inference have resulted in conflicting tree topologies, suggesting a close association of Dromas to members of different suborders and lineages within Charadriiformes. Here, we revisited the issue by applying Bayesian and parsimony methods of tree inference to 2,012 anatomical and 5,183 molecular characters to a set of 22 shorebird genera (including Turnix). Our results suggest that Bayesian analysis of anatomical characters does not resolve the phylogenetic relationship of shorebirds with strong statistical support. In contrast, Bayesian and parsimony tree inference from molecular data provided much stronger support for the phylogenetic relationships within shorebirds, and support a sister relationship of Dromas to Glareolidae (pratincoles and coursers), in agreement with previously published DNA-DNA hybridization studies.     

A fossil brain from the Cretaceous of European Russia and avian sensory evolution

Fossils preserving traces of soft anatomy are rare in the fossil record; even rarer is evidence bearing on the size and shape of sense organs that provide us with insights into mode of life. Here, we describe unique fossil preservation of an avian brain from the Volgograd region of European Russia. The brain of this Melovatka bird is similar in shape and morphology to those of known fossil ornithurines (the lineage that includes living birds), such as the marine diving birds Hesperornis and Enaliornis, but documents a new stage in avian sensory evolution: acute nocturnal vision coupled with well-developed hearing and smell, developed by the Late Cretaceous (ca 90Myr ago). This fossil also provides insights into previous 'bird-like' brain reconstructions for the most basal avian Archaeopteryx--reduction of olfactory lobes (sense of smell) and enlargement of the hindbrain (cerebellum) occurred subsequent to Archaeopteryx in avian evolution, closer to the ornithurine lineage that comprises living birds. The Melovatka bird also suggests that brain enlargement in early avians was not correlated with the evolution of powered flight.     

Heritable circadian period length in a wild bird population

Timing is essential, but circadian clocks, which play a crucial role in timekeeping, are almost unaddressed in evolutionary ecology. A key property of circadian clocks is their free-running period length (τ), i.e. the time taken for a full cycle under constant conditions. Under laboratory conditions, concordance of τ with the ambient light–dark cycle confers major fitness benefits, but little is known about period length and its implications in natural populations. We therefore studied natural variation of circadian traits in a songbird, the great tit (Parus major), by recording locomotor activity of 98 hand-raised, wild-derived individuals. We found, unexpectedly, that the free-running period of this diurnal species was significantly shorter than 24 h in constant dim light. We furthermore demonstrate, to our knowledge for the first time in a wild vertebrate, ample genetic variation and high heritability (h² = 0.86 ± 0.24), implying that period length is potentially malleable by micro-evolutionary change. The observed, short period length may be a consequence of sexual selection, as offspring from extra-pair matings had significantly shorter free-running periods than their half-siblings from within-pair matings. These findings position circadian clocks in the ‘real world’ and underscore the value of using chronobiological approaches in evolutionary ecology. Evolutionary ecologists study variation and its fitness consequences, but often have difficulties relating behavioural variation to physiological mechanisms. The findings presented here open the possibility that properties of internal, circadian clocks affect performance in traits that are relevant to fitness and sexual selection.     

Cumulative t-link threshold models for the genetic analysis of calving ease scores

In this study, a hierarchical threshold mixed model based on a cumulative t-link specification for the analysis of ordinal data or more, specifically, calving ease scores, was developed. The validation of this model and the Markov chain Monte Carlo (MCMC) algorithm was carried out on simulated data from normally and t₄ (i.e. a t-distribution with four degrees of freedom) distributed populations using the deviance information criterion (DIC) and a pseudo Bayes factor (PBF) measure to validate recently proposed model choice criteria. The simulation study indicated that although inference on the degrees of freedom parameter is possible, MCMC mixing was problematic. Nevertheless, the DIC and PBF were validated to be satisfactory measures of model fit to data. A sire and maternal grandsire cumulative t-link model was applied to a calving ease dataset from 8847 Italian Piemontese first parity dams. The cumulative t-link model was shown to lead to posterior means of direct and maternal heritabilities (0.40 ± 0.06, 0.11 ± 0.04) and a direct maternal genetic correlation (-0.58 ± 0.15) that were not different from the corresponding posterior means of the heritabilities (0.42 ± 0.07, 0.14 ± 0.04) and the genetic correlation (-0.55 ± 0.14) inferred under the conventional cumulative probit link threshold model. Furthermore, the correlation (> 0.99) between posterior means of sire progeny merit from the two models suggested no meaningful rerankings. Nevertheless, the cumulative t-link model was decisively chosen as the better fitting model for this calving ease data using DIC and PBF.     

Plausibility of inferred ancestral phenotypes and the evaluation of alternative models of limb evolution in scincid lizards

Phylogenetic approaches to inferring ancestral character states are becoming increasingly sophisticated; however, the potential remains for available methods to yield strongly supported but inaccurate ancestral state estimates. The consistency of ancestral states inferred for two or more characters affords a useful criterion for evaluating ancestral trait reconstructions. Ancestral state estimates for multiple characters that entail plausible phenotypes when considered together may reasonably be assumed to be reliable. However, the accuracy of inferred ancestral states for one or more characters may be questionable where combined reconstructions imply implausible phenotypes for a proportion of internal nodes. This criterion for assessing reconstructed ancestral states is applied here in evaluating inferences of ancestral limb morphology in the scincid lizard clade Lerista. Ancestral numbers of digits for the manus and pes inferred assuming the models that best fit the data entail ancestral digit configurations for many nodes that differ fundamentally from configurations observed among known species. However, when an alternative model is assumed for the pes, inferred ancestral digit configurations are invariably represented among observed phenotypes. This indicates that a suboptimal model for the pes (and not the model providing the best fit to the data) yields accurate ancestral state estimates.