Diversity, distribution and intrinsic extinction vulnerability of exploited marine bivalves.

Marine bivalves are important components of ecosystems and exploited by humans for food across the world, but the intrinsic vulnerability of exploited bivalve species to global changes is poorly known. Here, we expand the list of shallow-marine bivalves known to be exploited worldwide, with 720 exploited bivalve species added beyond the 81 in the United Nations FAO Production Database, and investigate their diversity, distribution and extinction vulnerability using a metric based on ecological traits and evolutionary history. The added species shift the richness hotspot of exploited species from the northeast Atlantic to the west Pacific, with 55% of bivalve families being exploited, concentrated mostly in two major clades but all major body plans. We find that exploited species tend to be larger in size, occur in shallower waters, and have larger geographic and thermal ranges-the last two traits are known to confer extinction-resistance in marine bivalves. However, exploited bivalve species in certain regions such as the tropical east Atlantic and the temperate northeast and southeast Pacific, are among those with high intrinsic vulnerability and are a large fraction of regional faunal diversity. Our results pinpoint regional faunas and specific taxa of likely concern for management and conservation.

Cambrian origin but no early burst in functional disparity for Class Bivalvia.

Both the Cambrian explosion, more than half a billion years ago, and its Ordovician aftermath some 35 Myr later, are often framed as episodes of widespread ecological opportunity, but not all clades originating during this interval showed prolific rises in morphological or functional disparity. In a direct analysis of functional disparity, instead of the more commonly used proxy of morphological disparity, we find that ecological functions of Class Bivalvia arose concordantly with and even lagged behind taxonomic diversification, rather than the early-burst pattern expected for clades originating in supposedly open ecological landscapes. Unlike several other clades originating in the Cambrian explosion, the bivalves' belated acquisition of key anatomical novelties imposed a macroevolutionary lag, and even when those novelties evolved in the Early Ordovician, functional disparity never surpassed taxonomic diversity. Beyond this early period of animal evolution, the founding and subsequent diversification of new major clades and their functions might be expected to follow the pattern of the early bivalves-one where interactions between highly dynamic environmental and biotic landscapes and evolutionary contingencies need not promote prolific functional innovation.

Is species richness mediated by functional and genetic divergence? A global analysis in birds.

Unravelling why species richness shows such dramatic spatial variation is an ongoing challenge. Common to many theories is that increasing species richness (e.g. with latitude) requires a compensatory trade-off on an axis of species' ecology. Spatial variation in species richness may also affect genetic diversity if large numbers of coexisting, related species result in smaller population sizes.Here, we test whether increasing species richness results in differential occupation of morphospace by the constituent species, or decreases species' genetic diversity. We test for two potential mechanisms of morphological accommodation: denser packing in ecomorphological space, and expansion of the space. We then test whether species differ in their nucleotide diversity depending on allopatry or sympatry with relatives, indicative of potential genetic consequences of coexistence that would reduce genetic diversity in sympatry. We ask these questions in a spatially explicit framework, using a global database of avian functional trait measurements in combination with >120,000 sequences downloaded from GenBank.We find that higher species richness within families is not systematically correlated with either packing in morphological space or overdispersion but, at the Class level, we find a general positive relationship between packing and species richness, but that points sampled in the tropics have comparatively greater packing than temperate ones relative to their species richness. We find limited evidence that geographical co-occurrence with closely related species or tropical distributions decreases nucleotide diversity of nuclear genes; however, this requires further analysis.Our results suggest that avian families can accumulate species regionally with minimal tradeoffs or cost, implying that external biotic factors do not limit species richness. Read the free Plain Language Summary for this article on the Journal blog.

Climatic refugia and reduced extinction correlate with underdispersion in mammals and birds in Africa.

Macroevolutionary patterns, often inferred from metrics of community relatedness, are often used to ascertain major evolutionary processes shaping communities. These patterns have been shown to be informative of biogeographic barriers, of habitat suitability and invasibility (especially with regard to environmental filtering), and of regions that function as evolutionary cradles (i.e., sources of diversification) or museums (i.e., regions of reduced extinction). Here, we analyzed continental datasets of mammal and bird distributions to identify primary drivers of community evolution on the African continent for mostly endothermic vertebrates. We find that underdispersion (i.e., relatively low phylogenetic diversity compared to species richness) closely correlates with specific ecoregions that have been identified as climatic refugia in the literature, regardless of whether these specific regions have been touted as cradles or museums. Using theoretical models of identical communities that differ only with respect to extinction rates, we find that even small suppressions of extinction rates can result in underdispersed communities, supporting the hypothesis that climatic stability can lead to underdispersion. We posit that large-scale patterns of under- and overdispersion between regions of similar species richness are more reflective of a particular region's extinction potential, and that the very nature of refugia can lead to underdispersion via the steady accumulation of species richness through diversification within the same ecoregion during climatic cycles. Thus, patterns of environmental filtering can be obfuscated by environments that coincide with biogeographic refugia, and considerations of regional biogeographic history are paramount for inferring macroevolutionary processes.

The causes and ecological context of rapid morphological evolution in birds.

Episodic pulses in morphological diversification are a prominent feature of evolutionary history, driven by factors that remain widely disputed. Resolving this question has proved challenging because comprehensive species-level data are generally unavailable at sufficient scale. Combining global phylogenetic and morphological data for birds, we show that pulses of diversification in lineages and traits tend to occur independently and in different contexts. Speciation pulses are preceded by greater differentiation in overall morphology and habitat niche, then followed by increased rates of beak evolution. Contrary to standard hypotheses, pulses of morphological diversification tend to be associated with habitat niche stability rather than adaptation to different diets and habitat types. These patterns suggest that the timing of diversification varies across traits according to their ecological function, and that pulses of morphological evolution may occur when successful lineages subdivide niche space within particular habitat types. Our results highlight the growing potential of functional trait data sets to refine macroevolutionary models.

Evolutionary modularity, integration and disparity in an accretionary skeleton: analysis of venerid Bivalvia.

Modular evolution, the relatively independent evolution of body parts, may promote high morphological disparity in a clade. Conversely, integrated evolution via stronger covariation of parts may limit disparity. However, integration can also promote high disparity by channelling morphological evolution along lines of least resistance-a process that may be particularly important in the accumulation of disparity in the many invertebrate systems having accretionary growth. We use a time-calibrated phylogenetic hypothesis and high-density, three-dimensional semilandmarking to analyse the relationship between modularity, integration and disparity in the most diverse extant bivalve family: the Veneridae. In general, venerids have a simple, two-module parcellation of their body that is divided into features of the calcium carbonate shell and features of the internal soft anatomy. This division falls more along developmental than functional lines when placed in the context of bivalve anatomy and biomechanics. The venerid body is tightly integrated in absolute terms, but disparity appears to increase with modularity strength among subclades and ecologies. Thus, shifts towards more mosaic evolution beget higher morphological variance in this speciose family.

Calibrating phylogenies assuming bifurcation or budding alters inferred macroevolutionary dynamics in a densely sampled phylogeny of bivalve families.

Analyses of evolutionary dynamics depend on how phylogenetic data are time-scaled. Most analyses of extant taxa assume a purely bifurcating model, where nodes are calibrated using the daughter lineage with the older first occurrence in the fossil record. This contrasts with budding, where nodes are calibrated using the younger first occurrence. Here, we use the extensive fossil record of bivalve molluscs for a large-scale evaluation of how branching models affect macroevolutionary analyses. We time-calibrated 91% of nodes, ranging in age from 2.59 to 485 Ma, in a phylogeny of 97 extant bivalve families. Allowing budding-based calibrations minimizes conflict between the tree and observed fossil record, and reduces the summed duration of inferred 'ghost lineages' from 6.76 billion years (Gyr; bifurcating model) to 1.00 Gyr (budding). Adding 31 extinct paraphyletic families raises ghost lineage totals to 7.86 Gyr (bifurcating) and 1.92 Gyr (budding), but incorporates more information to date divergences between lineages. Macroevolutionary analyses under a bifurcating model conflict with other palaeontological evidence on the magnitude of the end-Palaeozoic extinction, and strongly reduce Cenozoic diversification. Consideration of different branching models is essential when node-calibrating phylogenies, and for a major clade with a robust fossil record, a budding model appears more appropriate.

Extinction rates of non-avian dinosaur species are uncorrelated with the rate of evolution of phylogenetically informative characters.

Determining the factors that shape temporal variation in species diversity is an ongoing challenge. One theory is that species exhibiting lower rates of phenotypic evolution should be more likely to go extinct as they are more susceptible to changing environmental conditions. However, little work has been done to assess whether this process shapes comparatively few lineages, or is a common mechanism shaping changes in species diversity. Here, I analyse the correlation between rates of morphological evolution and extinction at the species level using six published morphological matrices of non-avian dinosaurs. I find no correlation between the two rates at different taxonomic scales, suggesting that extinction in these groups is better described by other factors. As there is a strong prior expectation of correlated rates, I suggest that traditional morphological matrices are inappropriate for addressing this question and that the characters governing lineage persistence are independent of those with high phylogenetic signal. This may be comprehensively determined with continued development of phenomic matrices.

New mammalian and avian records from the late Eocene La Meseta and Submeseta formations of Seymour Island, Antarctica.

The middle-late Eocene of Antarctica was characterized by dramatic change as the continent became isolated from the other southern landmasses and the Antarctic Circumpolar Current formed. These events were crucial to the formation of the permanent Antarctic ice cap, affecting both regional and global climate change. Our best insight into how life in the high latitudes responded to this climatic shift is provided by the fossil record from Seymour Island, near the eastern coast of the Antarctic Peninsula. While extensive collections have been made from the La Meseta and Submeseta formations of this island, few avian taxa other than penguins have been described and mammalian postcranial remains have been scarce. Here, we report new fossils from Seymour Island collected by the Antarctic Peninsula Paleontology Project. These include a mammalian metapodial referred to Xenarthra and avian material including a partial tarsometatarsus referred to Gruiformes (cranes, rails, and allies). Penguin fossils (Sphenisciformes) continue to be most abundant in new collections from these deposits. We report several penguin remains including a large spear-like mandible preserving the symphysis, a nearly complete tarsometatarsus with similarities to the large penguin clade Palaeeudyptes but possibly representing a new species, and two small partial tarsometatarsi belonging to the genus Delphinornis. These findings expand our view of Eocene vertebrate faunas on Antarctica. Specifically, the new remains referred to Gruiformes and Xenarthra provide support for previously proposed, but contentious, earliest occurrence records of these clades on the continent.

Mass estimation of extinct taxa and phylogenetic hypotheses both influence analyses of character evolution in a large clade of birds (Telluraves).

Incorporating extinct taxa in phylogenetic comparative methods is rapidly becoming invaluable in studies of character evolution. An increasing number of studies have evaluated the effects of extinct taxa, and different numbers of extinct taxa, on model selection and parameter estimation. Body mass is a well-studied phenotype, but individual mass estimates may vary dramatically depending on the particular measurement used. Here, we perform an analysis of body mass evolution in a large clade of principally arboreal birds, incorporating 76 extinct species. We evaluate how different methods for estimating body mass of extinct taxa, and different phylogenetic hypotheses, affect our understanding of the rate and pattern of body mass evolution. Our results show that model selection can vary dramatically depending on the phenotypic and phylogenetic hypothesis used in the reconstruction. Even small changes in phenotype estimates can lead to different model selection and, as a result, affect the inferred evolutionary history. The best-fit models support an increase in the rate of evolution following the K-Pg boundary, with variation accumulating linearly through the Cenozoic. These results provide additional insight into the application of comparative models of evolution, as well as the evolutionary history of one of the most spectacular vertebrate radiations.

Speciation Rate Is Independent of the Rate of Evolution of Morphological Size, Shape, and Absolute Morphological Specialization in a Large Clade of Birds.

Whether ecological differences between species evolve in parallel with lineage diversification is a fundamental issue in evolutionary biology. These processes might be connected if conditions that favor the proliferation of species, such as release from competitors, facilitate the evolution of novel ecological relationships. Despite this, phylogenetic studies do not consistently identify such a connection. Conversely, if higher diversity caused species to become increasingly specialized ecologically, then lineage diversification might become dissociated from ecological diversification. In this analysis, we ask whether the rate of lineage diversification in a large clade of birds is correlated with morphological specialization and with rates of morphological evolution. We find that morphological variation is related to species richness within clades but that rates of morphological evolution are decoupled from the rate of lineage diversification. Additionally, morphological specialization within lineages is independent of the rate at which lineages diversify, with the results apparently robust against false negative inference. This dissociation is likely a consequence of the major ecomorphological differences between avian clades arising early in their evolutionary history, with comparatively little variation added subsequently, while avian diversification has been driven predominantly by geographic isolation and sexual selection. Accordingly, biodiversity appears to be limited by the extent to which taxa can subdivide exploited regions of ecological space and not just overall ecological opportunity.

Tip-dating and the origin of Telluraves.

Despite a relatively vast accumulation of molecular data, the timing of diversification of modern bird lineages remains elusive. Accurate dating of the origination of Telluraves-a clade of birds defined by their arboreality-is of particular interest, as it contains the most species-rich avian group, the passerines. Historically, neontological studies have estimated a Cretaceous origin for the group, but more recent studies have recovered Cenozoic dates, closer to the oldest known fossils for the group. We employ total-evidence dating to estimate divergence times that are expected to be both less sensitive to prior assumptions and more accurate. Specifically, we use a large collection of morphological character data from arboreal bird fossils, along with combined molecular sequence and morphological character data from extant taxa. Our analyses recover a Late Cretaceous origin for crown Telluraves, with a few lineages crossing the K-Pg boundary. Following the K-Pg boundary, our results show the group underwent rapid diversification, likely benefiting from increased ecological opportunities in the aftermath of the extinction event. We find very little confidence for the precise topological placement of many extinct taxa, possibly due to rapid diversification, paucity of character data, and rapid morphological differentiation during the early history of the group.

Oligocene origin and drivers of diversification in the genus Sticta (Lobariaceae, Ascomycota).

A major challenge to evolutionary biologists is to understand how biodiversity is distributed through space and time and across the tree of life. Diversification of organisms is influenced by many factors that act at different times and geographic locations but it is still not clear which have a significant impact and how drivers interact. To study diversification, we chose the lichen genus Sticta, by sampling through most of the global range and producing a time tree. We estimate that Sticta originated about 30 million years ago, but biogoegraphic analysis was unclear in estimating the origin of the genus. Furthermore, we investigated the effect of dispersal ability finding that Sticta has a high dispersal rate, as collections from Hawaii showed that divergent lineages colonized the islands at least four times. Symbiont interactions were investigated using BiSSE to understand if green-algal or cyanobacterial symbiont interactions influenced diversification, only to find that the positive results were driven almost completely by Type I error. On the other hand, another BiSSE analysis found that an association with Andean tectonic activity increases the speciation rate of species.

Structural equation modeling as a tool to investigate correlates of extra-pair paternity in birds.

Identifying relationships between variables in ecological systems is challenging due to the large number of interacting factors. One system studied in detail is avian reproduction, where molecular analyses have revealed dramatic variation in rates of extra-pair paternity-the frequency with which broods contain individuals sired by different males. Despite the attention the topic has received, identification of ecological predictors of the observed variation remains elusive. In this study we evaluate how structural equation modeling-which allows for simultaneous estimation of covariation between all variables in a model-can help identify significant relationships between ecological variables and extra-pair paternity. We estimated the correlation of eight different variables using data from 36 species of passerines by including them in six different models of varying complexity. We recover strong support for species with lower rates of male care having higher rates of extra-pair paternity. Our results also suggest that testes size, range size, and longevity all potentially have a relationship with rates of extra-pair paternity; however, interpretation of this result is more challenging. More generally, these results demonstrate the utility of applying structural equation modeling to understanding correlations among interacting variables in complex biological systems.

Selection on parental performance opposes selection for larger body mass in a wild population of blue tits.

There is abundant evidence in many taxa for positive directional selection on body size, and yet little evidence for microevolutionary change. In many species, variation in body size is partly determined by the actions of parents, so a proposed explanation for stasis is the presence of a negative genetic correlation between direct and parental effects. Consequently, selecting genes for increased body size would result in a correlated decline in parental effects, reducing body size in the following generation. We show that these arguments implicitly assume that parental care is cost free, and that including a cost alters the predicted genetic architectures needed to explain stasis. Using a large cross-fostered population of blue tits, we estimate direct selection on parental effects for body mass, and show it is negative. Negative selection is consistent with a cost to parental care, mainly acting through a reduction in current fecundity rather than survival. Under these conditions, evolutionary stasis is possible for moderately negative genetic correlations between direct and parental effects. This is in contrast to the implausibly extreme correlations needed when care is assumed to be cost-free. Thus, we highlight the importance of accounting correctly for complete selection acting on traits across generations.

Intraclutch differences in egg characteristics mitigate the consequences of age-related hierarchies in a wild passerine.

The relative age of an individual's siblings is a major cause of fitness variation in many species. In Blue tits (Cyanistes caeruleus), we show that age hierarchies are predominantly caused by incubation preclutch completion, such that last laid eggs hatch later than early laid eggs. However, after statistically controlling for incubation behavior late laid eggs are shown to hatch more quickly than early laid eggs reducing the amount of asynchrony. By experimentally switching early and late laid eggs between nests on the day they were laid, we controlled for the effect of differential incubation and found that the faster hatching times of late laid eggs remains. Chicks that hatched earlier were heavier and had higher probability of fledgling, and chicks that hatched from experimental eggs had patterns of growth and survival consistent with this. Egg mass explained a small part of this variation, but the remainder must be due to egg composition. These results are consistent with the idea that intrinsic differences between eggs across the laying sequence serve to mitigate the effects of age-related hierarchies. We also show that between-clutch variation in prenatal developmental rate exists and that it is mainly environmental in origin rather than genetic.

Disentangling genetic and prenatal sources of familial resemblance across ontogeny in a wild passerine.

Cross-fostering experiments are widely used by quantitative geneticists to study genetics and by behavioral ecologists to study the effects of prenatal investment. Generally, the effects of genes and prenatal investment are confounded and the interpretation given to such experiments is largely dependent on the interests of the researcher. Using a large-scale well-controlled experiment on a wild population of blue tits (Cyanistes caeruleus), we are able to partition variation in body mass across ontogeny into the effects of genes and the effects of between-clutch variation in egg characteristics. We show that although egg effects are important early in ontogeny they quickly dissipate, suggesting that the genetic interpretation of cross-fostering experiments may be preferable for many types of trait. However, the heritability of body mass is smaller than has previously been reported. Our results suggest that this is due to a combination of controlling postnatal environmental effects more carefully and accounting for viability selection operating early in ontogeny.

Jasmonate-induced epoxidation of tabersonine by a cytochrome P-450 in hairy root cultures of Catharanthus roseus.

Methyl jasmonate, a chemical inducer of secondary metabolism, was shown to promote tabersonine 2 biosynthesis in hairy root cultures of Catharanthus roseus. Tabersonine 6,7-epoxidase activity was detected in total protein extract of jasmonate-induced hairy root cultures using labeled 14C-tabersonine 2. This enzyme converted tabersonine 2 to lochnericine 3 by selective epoxidation at positions 6 and 7 via a reaction dependent on NADPH and molecular oxygen. Carbon monoxide, clotrimazole, miconazole, and cytochrome C were shown to be strong inhibitors of the enzyme. The activity was found in microsomes, indicating that tabersonine 6,7-epoxidase was a cytochrome P-450-dependent monooxygenase.