Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes

The International Crocodilian Genomes Working Group (ICGWG) will sequence and assemble the American alligator (Alligator mississippiensis), saltwater crocodile (Crocodylus porosus) and Indian gharial (Gavialis gangeticus) genomes. The status of these projects and our planned analyses are described.     

Loss of carpal elements in crocodilian limb evolution: morphogenetic model corroborated by palaeobiological data

The comparison of bone homology between the manus of an Early Cretaceous fossil crocodile and that of the extant species Alligator mississippiensis supports explicidy, for the first time, the hypothesis of carpal loss in crocodilian limb evolution. This hypothesis, based on a developmental model of the organization of the tetrapod limb, is in accordance with the fossil evidence, and may supersede traditional Haeckelian views based on recapitulatory paradigms. The homologous relationships of carpal elements reveal the existence of two carpal patterns- one plesiomorphic and one apomorphic-in the crocodilian lineage. Phylogenetic change is explained causally by alterations of the osteogenesis of the distal carpals 2 and 3, which remain unossified in extant crocodile adults. This implies that crocodilian limb evolution is constrained by a process of paedomorphosis. This modification of the architecture of the crocodilian hand is a terminal event of its evolutionary history, affecting only eusuchian crocodiles. The results of this study contest the traditional view that the skeletal pattern of the crocodilian limb has been conserved unchanged since the Triassic.     

Patterns of morphospace occupation and mechanical performance in extant crocodilian skulls: A combined geometric morphometric and finite element modeling approach

Extant and fossil crocodilians have long been divided into taxonomic and/or ecological groups based on broad patterns of skull shape, particularly the relative length and width of the snout. However, these patterns have not been quantitatively analyzed in detail, and their biomechanical and functional implications are similarly understudied. Here, we use geometric morphometrics and finite element analysis to explore the patterns of variation in crocodilian skull morphology and the functional implications of those patterns. Our results indicate that skull shape variation in extant crocodiles is much more complex than previously recognized. Differences in snout length and width are the main components of shape variation, but these differences are correlated with changes in other regions of the skull. Additionally, there is considerable disparity within general classes such as longirostrine and brevirostrine forms. For example, Gavialis and Tomistoma occupy different parts of morphospace implying a significant difference in skull shape, despite the fact that both are traditionally considered longirostrine. Skull length and width also strongly influence the mechanical performance of the skull; long and narrow morphotypes (e.g., Tomistoma) experience the highest amount of stress during biting, whereas short and broad morphotypes (e.g., Caiman latirostris) experience the least amount of stress. Biomechanical stress and the hydrodynamic properties of the skull show a strong relationship with the distribution of crocodilians in skull morphospace, whereas phylogeny and biogeography show weak or no correlation. Therefore, ecological specializations related to feeding and foraging likely have the greatest influence on crocodilian skull shape. J. Morphol., 2008. © 2008 Wiley‐Liss, Inc.     

The evolution of crocodilian nesting ecology and behavior

Crocodilians comprise an ancient and successful lineage of archosaurs that repeatedly raises questions on how they survived a mass extinction and remained relatively unchanged for ~100 million years. Was their success due to the change‐resistant retention of a specific set of traits over time (phylogenetic conservatism) or due to flexible, generalist capabilities (e.g., catholic diets, phenotypic plasticity in behavior), or some combination of these? We examined the evolution of reproductive ecology and behavior of crocodilians within a phylogenetic perspective, using 14 traits for all 24 species to determine whether these traits were phylogenetically constrained versus (ecologically) convergent. Our analysis revealed that the ancestral crocodilian was a mound nester that exhibited both nest attendance and defense. Nesting mode exhibited 4–5 transformations from mound to hole nesting, a convergence of which habitat may have been a driving factor. Hole nesters were more likely to nest communally, but this association may be biased by scale. Although there were exceptions, mound nesters typically nested during the wet season and hole nesters during the dry season; this trait was relatively conserved, however. About two‐thirds of species timed their nesting with the wet season, while the other third timed their hatching with the onset of the wet season. Nest attendance and defense were nearly ubiquitous and thus exhibited phylogenetic conservatism, but attendance lodging was diverse among species, showing multiple reversals between water and burrows. Collectively, our analysis reveals that reproductive trait evolution in crocodilians reflects phylogenetic constraint (nest attendance, nest defense), ecological convergence (seasonal timing of nesting, nest attendance lodging), or both (mode of nesting). Some traits (e.g., communal nesting and mode of nesting) were autocorrelated. Our analysis provides a framework for addressing hypotheses raised for why there has been trait convergence in reproductive ecology and behavior in crocodilians and why some traits remained phylogenetically conserved.     

Patterns of correlated character evolution in flightless birds: a phylogenetic approach

Given a robust phylogeny for a particular higher taxon, it is possible to map the evolution of various character changes onto the phylogeny and study the extent to which they co-occur. Of particular interest are the questions of (a) whether particular morphological changes tend to accompany changes in ecology or behaviour to which they bear a functional relationship and (b) whether changes in those ‘primary’ morphological characters tend to be associated with correlated changes in other aspects of morphology, as would be expected given the high level of morphological integration that characterizes most organisms. Here we report a study of this kind, looking at morphological correlates of the evolution of flightlessness in birds, and using the concentrated changes test to determine whether associations are significant. We find that pectoral reduction, pelvic enlargement and changes in skull morphology significantly co-occur, and that these are usually achieved through heterochrony rather than other kinds of developmental reprogramming. This revised version was published online in November 2006 with corrections to the Cover Date.     

Repeated evolution of male sacrifice behavior in spiders correlated with genital mutilation

According to sexual cannibalism theory, male complicity in terminal mating can be adaptive when the male's future reproductive value is low relative to the benefits of self sacrifice. Spiders and insects that exhibit male sacrifice behavior (either complicity in cannibalism or spontaneous death associated with copulation) often also have male genitalia that stereotypically become broken or disfigured the first time they are used for copulation, potentially lowering his future reproductive value. Theoretical work on monogamy has identified male bias in the effective sex ratio as a precursor to the evolution of monogamy (including male sacrifice) as an adaptive form of paternity protection. Using phylogeny-based statistics and drawing on several phylogenetic studies of araneoid spiders, I investigate relationships between male sacrifice behavior, genital mutilation, extreme sexual size dimorphism, and the accumulation of multiple males in the female web (as an indicator of a male-based effective sex ratio). This investigation focuses on araneoid spiders because several independent origins of sacrifice behavior are known for this group and the phylogenetic structure of the lineage is relatively well studied. I report that male genital mutilation is significantly correlated with sacrifice behavior and argue that this finding is consistent with sexual cannibalism theory. Male sacrifice behavior is also correlated with male accumulation, a result that is consistent with theoretical work on the evolution of monogamy. Male accumulation and extreme sexual size dimorphism are correlated suggesting that sex-based differences in maturation time can lead to a male biased effective sex ratio. Similar patterns of correlated characters may hold for some insect taxa. Studying traits that have appeared independently in multiple lineages is a powerful method for developing general theories about the evolution of biological phenomena.     

Repetitive sequences in the crocodilian mitochondrial control region: poly-A sequences and heteroplasmic tandem repeats

Heteroplasmic tandem repeats in the mitochondrial control region have been documented in a wide variety of vertebrate species. We have examined the control region from 11 species in the family Crocodylidae and identified two different types of heteroplasmic repetitive sequences in the conserved sequence block (CSB) domain-an extensive poly-A tract that appears to be involved in the formation of secondary structure and a series of tandem repeats located downstream ranging from approximately 50 to approximately 80 bp in length. We describe this portion of the crocodylian control region in detail and focus on members of the family Crocodylidae. We then address the origins of the tandemly repeated sequences in this family and suggest hypotheses to explain possible mechanisms of expansion/contraction of the sequences. We have also examined control region sequences from Alligator and Caiman and offer hypotheses for the origin of tandem repeats found in those taxa. Finally, we present a brief analysis of intraindividual and interindividual haplotype variation by examining representatives of Morelet's crocodile (Crocodylus moreletii).     

Variation in crocodilian dorsal scute organization and geometry with a discussion of possible functional implications

Dermal ossifications, including osteoderms, are present in many vertebrates and are frequently interpreted as a defense against predators. Nevertheless, osteoderms remain ubiquitous in adult crocodilians while being absent in hatchlings, even though adults rarely experience predation. In other biological systems, increased variation, particularly fluctuating asymmetry, have proven useful for identifying biological structures likely to have evolved under relaxed selection, which in turn may inform their function. Therefore, using the keratinous scutes as proxies for the underlying osteoderm morphology, I investigated the average intraspecific variability of geometry and fluctuating asymmetry in dorsal scutes in five species of crocodilians. I first tested for differences in variability of scute length and width, then for differences in bilateral fluctuating asymmetry of scute number, before finally investigating scute distribution patterns for each species compared to hypothetical rectangular and hexagonal scute arrangements. The American crocodile, Crocodylus acutus, shows significantly more asymmetry than other species, which is consistent with relaxed selection on osteoderms in this species. A suspected decrease in intraspecific aggression within Crocodylus acutus, in conjunction with the inferred relaxed selection, suggests that, in general, crocodilian osteoderms function primarily as defensive armor in aggressive encounters with conspecifics. The smooth‐fronted caiman, Paleosuchus trigonatus, exhibits increased variation in scute dimensions linked to the mediolateral offset of osteoderms in adjacent rows, possibly resulting in a more rigid carapace. Unfortunately, comparative data on crocodilian behavior, physiology, and development is extremely limited and restricts the ability to explore other potential explanations for the patterns observed, highlighting the need for more research on rare and cryptic crocodylians.     

小麦籽粒品质性状的杂种优势和相关分析

以6个小麦品种（系）组配的6个杂交组合F1为供试材料,对其籽粒品质性状进行了杂种优化、性状相关和亲子相关分析。结果表明：（1）粉质参数中的形成时间和稳定时间杂种优势最强,分别为56.49％和32.23％;籽粒蛋白质含量和硬度的优势最弱,分别为-2.73％和-0.9046％;沉淀值和湿面筋含量的优势居中,分别为6.88％和5.88％。（2）粉质参数中的吸水率、稳定时间同其它几个指标之间呈显著或极显著相关;沉淀值与籽粒蛋白质含量呈正相关,但不显著,与湿面筋含量呈显著负相关;湿面筋含量与籽粒蛋白质含量呈显著负相关。（3）杂种F1的籽粒Zeleny沉淀值与高亲值,低亲值和中亲值呈显著和极显著正相关;籽粒蛋白质含量和湿面筋含量与高亲值,低亲值和中亲值呈负相关或不相关。     

Braincase evolution in suchian archosaurs (Reptilia: Diapsida): evidence from the rauisuchian Batrachotomus kupferzellensis

The osteology of an almost complete braincase of the rauisuchian archosaur Batrachotomus kupferzellensis Gower from the Middle Triassic of Germany is described. There is a possibly discrete epiotic ossification, the metotic fissure is undivided by bone (i.e. there is a metotic foramen), the medial wall of the otic capsule is mostly ossified, the cerebral branch of the internal carotid artery entered the lateral surface of the parabasisphenoid, the ventral ramus of the opisthotic is more prominent laterally than a strong subvertical ridge on the exoccipital and basioccipital that lies posterior to the external foramen for the hypoglossal nerve, and the perilymphatic foramen faces away from the otic capsule in a posterior direction. Braincase morphology in the rauisuchians Saurosuchus galilei , Postosuchus kirkpatricki, and Tikisuchus romeri is reviewed. A matrix of 27 braincase characters for 12 archosaurian taxa is analysed. The most parsimonious hypothesis is consistent with the currently orthodox view of archosaurian phylogeny, except in that aetosaurians are more closely related to crocodylomorphs than is any rauisuchian. This phylogeny is used in a brief interpretation of the evolution of derived braincase features present in extant crocodilians. © 2002 The Linnean Society of London, Zoological Journal of the Linnean Society , 2002, 136 , 49–76.     

Behavioral syndromes and the evolution of correlated behavior in zebrafish

Studies of "behavioral syndromes" in different populations andspecies of animals can be used to shed light on the underlyingmechanisms of evolution. For example, some personality syndromessuggest the existence of an underlying hormonal link, whereasother relationships between boldness and aggression appear tobe the result of similar selective pressures. Here, we used1 wild-derived and 2 laboratory strains of zebrafish (Daniorerio) to examine relationships among 5 behavioral measures:shoaling, activity level, predator approaches, latency to feedafter a disturbance, and biting to a mirror stimulus. We foundevidence of an activity syndrome, as if underlying metaboliccosts influence variation in multiple forms of behavior. Evidencefor a relationship between boldness and aggression was alsoapparent but depended both on strain and which specific behaviorpatterns were identified as measures of "boldness." Althoughsome comparisons of laboratory and wild-derived strains wereconsistent with a domestication syndrome, others were not. Mostobserved relationships were relatively weak and occasionallyinconsistent, arguing against strong underlying genetic linkagesor pleiotropic effects relating any of the behavioral measures.Instead, it may be more important to study the details of selectivecontext or the long-term impact of linkages between some, butnot all, of a large set of genes influencing complex behavioraltraits. We found profound differences among strains in mostbehavior patterns, but few sex differences. One strain (TM1)was consistently different from the others (SH and Nadia) beingmore social, more likely to approach predators, and taking lesstime to recover from disturbance than were the other 2 strains.     

Cranial capacity in hominid evolution

We present an analysis of cranial capacity of 118 hominid crania available from the literature. The crania belong to both the genusAustralopithecus andHomo and provide a clear outline of hominid cranial evolution starting at more than 3 million years ago. Beginning withA. afarensis there is a clear increase in both absolute and relative brain size with every successive time period.H.s. neandertal has an absolutely and relatively smaller brain size (1412cc, E.Q.=5.6) than fossil modernH.s. sapiens (1487cc, E.Q.=5.9). Three evolutionary models of hominid brain evolution were tested: gradualism, punctuated equilibrium, and a mixed model using both gradualism and punctuated equilibrium. Both parametric and non-parametric analyses show a clear trend toward increasing brain size withH. erectus and a possible relationship within archaicH. sapiens. An evolutionary stasis in cranial capacity could not be refuted for all other taxa. Consequently, the mixed model appears to more fully explain hominid cranial capacity evolution. However, taxonomic decisions could directly compromise the possibility of testing the evolutionary mechanisms hypothesized to be operating in hominid brain expansion.     

A phylogenetic model for investigating correlated evolution of substitution rates and continuous phenotypic characters

The comparative approach is routinely used to test for possible correlations between phenotypic or life-history traits. To correct for phylogenetic inertia, the method of independent contrasts assumes that continuous characters evolve along the phylogeny according to a multivariate Brownian process. Brownian diffusion processes have also been used to describe time variations of the parameters of the substitution process, such as the rate of substitution or the ratio of synonymous to nonsynonymous substitutions. Here, we develop a probabilistic framework for testing the coupling between continuous characters and parameters of the molecular substitution process. Rates of substitution and continuous characters are jointly modeled as a multivariate Brownian diffusion process of unknown covariance matrix. The covariance matrix, the divergence times and the phylogenetic variations of substitution rates and continuous characters are all jointly estimated in a Bayesian Monte Carlo framework, imposing on the covariance matrix a prior conjugate to the Brownian process so as to achieve a greater computational efficiency. The coupling between rates and phenotypes is assessed by measuring the posterior probability of positive or negative covariances, whereas divergence dates and phenotypic variations are marginally reconstructed in the context of the joint analysis. As an illustration, we apply the model to a set of 410 mammalian cytochrome b sequences. We observe a negative correlation between the rate of substitution and mass and longevity, which was previously observed. We also find a positive correlation between ω = dN/dS and mass and longevity, which we interpret as an indirect effect of variations of effective population size, thus in partial agreement with the nearly neutral theory. The method can easily be extended to any parameter of the substitution process and to any continuous phenotypic or environmental character.     

Co‐evolution of plumage characteristics and winter sociality in New and Old World sparrows

Understanding the evolution of phenotypic diversity, including the stunning array of avian plumage characters, is a central goal of evolutionary biology. Here, we applied a comparative analysis to test factors associated with the origin and maintenance of black chest and throat patches, which in some taxa are referred to as ‘badges‐of‐status’. Specifically, we tested whether the evolution of black colour patches in Old and New World sparrows is consistent with a signalling function during the nonbreeding season or breeding season. We found no positive associations between patch evolution and polygyny or summer sociality. Instead, patch evolution is significantly associated with sociality during the nonbreeding season. Additionally, unlike typical plumage characteristics under sexual selection, these patches are visible throughout the nonbreeding season. Further, the pattern of patch dimorphism uncovered in this study does not match expectations for a trait that evolved in a reproductive context. In particular, patch dimorphism is not associated with polygyny or the presence of extra‐pair mating although other types of plumage dimorphism are strongly associated with nonmonogamous mating systems. Overall, patterns of patch evolution suggest that they are more strongly associated with social competition during the nonbreeding season than sexual competition during the breeding season. These results clarify why some previous work has uncovered puzzling relationships between black plumage patches and reproductive behaviour. We discuss these findings in the context of signal theory and previous work on badges‐of‐status.     

Diversity and evolution of male secondary sexual characters in African squeakers and long-fingered frogs

The African frog genera Arthroleptis and Cardioglossa are unique among vertebrates in having males with extremely long third fingers. In some species, this sexual dimorphism is impressive, with male third fingers approaching 40% of body length. However, the diversity of this trait has not been documented thoroughly and several species appear to lack this trait. The present study documents the diversity of male secondary sexual traits in Arthroleptis and Cardioglossa , including elongate third fingers and digital and inguinal spines. Furthermore, it explores hypotheses of trait evolution, including explanations for the absence of male traits. Analyses of covariance suggest that the functional relationship between finger length and snout–vent length (SVL), both within and among species, is different for male finger III than for male fingers I, II, and IV, or for female finger III. Ancestral state reconstruction suggests that all male traits were present in the most recent common ancestor of Arthroleptis and Cardioglossa and that reduction or loss of traits occurred later. Across species, independent contrast analyses find no correlation between SVL and either male relative third digit length or dimorphism in relative third digit length. The number of spines on male fingers II and III are positively correlated but spine number is not correlated with SVL and only weakly correlated with relative third digit length. The diversity of male traits is evolutionarily labile and is not explained by simple hypotheses of character evolution. Arthroleptis and Cardioglossa may thus provide an interesting study system for understanding how changes in sexual selection forces produce male trait diversity.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 96 , 553–573.     

Correlation between the size,shape and position of the teeth on the jaws and the bite force in Theropoda

Theropods have fascinated both paleontologists and the general public due to their large diversity of sizes and morphologies. They also present a large variation in tooth morphologies. Previous studies have estimated the bite force of several specimens. The goal of this study is to determine if there is a correlation between the tooth size, shape and position on the skull and mandible and the bite force of these dinosaurs. Measurements were made on several theropods, including the bending strength of the teeth on the anterior-posterior and the mediolateral axes of the jaws, as well as the bending strength of the mandible, and were compared to fossil and modern Crocodylia. We observed that several bending strength maxima of the teeth trends were aligned with key areas of the mandible, and that the size, shape as well as the position of the teeth on the jaws were correlated with the bite force of both Crocodylia and theropods, which can be related to their diet and feeding habits.     

Habitat variation and wing coloration affect wing shape evolution in dragonflies

Habitats are spatially and temporally variable, and organisms must be able to track these changes. One potential mechanism for this is dispersal by flight. Therefore, we would expect flying animals to show adaptations in wing shape related to habitat variation. In this work, we explored variation in wing shape in relation to preferred water body (flowing water or standing water with tolerance for temporary conditions) and landscape (forested to open) using 32 species of dragonflies of the genus Trithemis (80% of the known species). We included a potential source of variation linked to sexual selection: the extent of wing coloration on hindwings. We used geometric morphometric methods for studying wing shape. We also explored the phenotypic correlation of wing shape between the sexes. We found that wing shape showed a phylogenetic structure and therefore also ran phylogenetic independent contrasts. After correcting for the phylogenetic effects, we found (i) no significant effect of water body on wing shape; (ii) male forewings and female hindwings differed with regard to landscape, being progressively broader from forested to open habitats; (iii) hindwings showed a wider base in wings with more coloration, especially in males; and (iv) evidence for phenotypic correlation of wing shape between the sexes across species. Hence, our results suggest that natural and sexual selection are acting partially independently on fore‐ and hindwings and with differences between the sexes, despite evidence for phenotypic correlation of wing shape between males and females.     

Evolution of egg target size: an analysis of selection on correlated characters

In broadcast-spawning marine organisms, chronic sperm limitation should select for traits that improve chances of sperm-egg contact. One mechanism may involve increasing the size of the physical or chemical target for sperm. However, models of fertilization kinetics predict that increasing egg size can reduce net zygote production due to an associated decline in fecundity. An alternate method for increasing physical target size is through addition of energetically inexpensive external structures, such as the jelly coats typical of eggs in species from several phyla. In selection experiments on eggs of the echinoid Dendraster excentricus, in which sperm was used as the agent of selection, eggs with larger overall targets were favored in fertilization. Actual shifts in target size following selection matched quantitative predictions of a model that assumed fertilization was proportional to target size. Jelly volume and ovum volume, two characters that contribute to target size, were correlated both within and among females. A cross-sectional analysis of selection partitioned the independent effects of these characters on fertilization success and showed that they experience similar direct selection pressures. Coupled with data on relative organic costs of the two materials, these results suggest that, under conditions where fertilization is limited by egg target size, selection should favor investment in low-cost accessory structures and may have a relatively weak effect on the evolution of ovum size.