Michael W. Hart

Things fall apart: biological species form unconnected parsimony networks

The generality of operational species definitions is limited by problematic definitions of between-species divergence. A recent phylogenetic species concept based on a simple objective measure of statistically significant genetic differentiation uses between-species application of statistical parsimony networks that are typically used for population genetic analysis within species. Here we review recent phylogeographic studies and reanalyse several mtDNA barcoding studies using this method. We found that (i) alignments of DNA sequences typically fall apart into a separate subnetwork for each Linnean species (but with a higher rate of true positives for mtDNA data) and (ii) DNA sequences from single species typically stick together in a single haplotype network. Departures from these patterns are usually consistent with hybridization or cryptic species diversity.

Quantifying Rates of Evolutionary Adaptation in Response to Ocean Acidification

The global acidification of the earths oceans is predicted to impact biodiversity via physiological effects impacting growth, survival, reproduction, and immunology, leading to changes in species abundances and global distributions. However, the degree to which these changes will play out critically depends on the evolutionary rate at which populations will respond to natural selection imposed by ocean acidification, which remains largely unquantified. Here we measure the potential for an evolutionary response to ocean acidification in larval development rate in two coastal invertebrates using a full-factorial breeding design. We show that the sea urchin species Strongylocentrotus franciscanus has vastly greater levels of phenotypic and genetic variation for larval size in future CO2 conditions compared to the mussel species Mytilus trossulus. Using these measures we demonstrate that S. franciscanus may have faster evolutionary responses within 50 years of the onset of predicted year-2100 CO2 conditions despite having lower population turnover rates. Our comparisons suggest that information on genetic variation, phenotypic variation, and key demographic parameters, may lend valuable insight into relative evolutionary potentials across a large number of species.

MOLECULAR PHYLOGENETIC ANALYSIS OF LIFE-HISTORY EVOLUTION IN ASTERINID STARFISH

We analyzed phylogenetic relationships among 12 nominal species of starfish in the genera Patiriella and Asterina (Order Valvatida, Family Asterinidae), based on complete sequences for a mitochondrial protein coding gene (cytochrome oxidase subunit I) and five mitochondrial transfer RNA genes (alanine, leucine, asparagine, glutamine, and proline) (1923 bp total). The resulting phylogeny was used to test a series of hypotheses about the evolution of life‐history traits. (1) A complex, feeding, planktonic larva is probably ancestral for these starfish, but this is not the most parsimonious reconstruction of ancestral larval states. (2) The feeding larval form was lost at least four times among these species, and three of these losses occurred among members of a single clade. (3) Small adult size evolved before both cases of hermaphroditism and viviparous brooding, but viviparity was not always preceded by an intermediate form of external brooding. (4) An ordered transformation series from feeding planktonic development to viviparous brooding has been predicted for starfish, but we could not find an example of this transformation series. (5) Viviparity evolved recently (< 2 Mya). (6) Both species selection and transformation of lineages may have contributed to the accumulation of species with nonfeeding development among these starfish. (7) Neither Asterina nor Patiriella are monophyletic genera. Larval forms and life‐history traits of these starfish have evolved freely under no obvious constraints, contrary to the widely assumed evolutionary conservatism of early development.

Functional Consequences of Phenotypic Plasticity in Echinoid Larvae

Phenotypic plasticity in feeding structures has been described for several larvae of marine invertebrates, including four species of echinoids. In these echinoids, larvae grown with scarce food grow a longer ciliated band than larvae grown with abundant food. Such phenotypic plasticity may be functionally significant if longer ciliated bands permit higher feeding rates when food is scarce. We replicate an earlier result showing that larvae of a sand dollar, Dendraster excentricus, grow longer ciliated bands in culture with scarce food. We show that these larvae can capture suspended food particles at the tips of longer arms, and that longer ciliated bands result in higher maximum clearance rates. The maximum clearance rate is enhanced by this phenotypic plasticity both early and late in larval life. However, longer ciliated bands did not completely compensate for reduced food supply: larvae grown with scarce food needed more time to complete larval development and metamorphosed into smaller juvenile sand dollars relative to larvae grown with abundant food.

The complex analytical landscape of gene flow inference

Gene flow estimation is essential for characterizing local adaptation, speciation potential and connectivity among threatened populations. New model-based population genetic methods can resolve complex demographic histories, but many studies in fields such as landscape genetics continue to rely on simple rules of thumb focused on gene flow to explain patterns of spatial differentiation. Here, we show how methods that use gene genealogies can reveal cryptic demographic histories and provide better estimates of gene flow with other parameters that contribute to genetic variation across landscapes and seascapes. We advocate for the expanded use and development of methods that consider spatial differentiation as the product of multiple forces interacting over time, and caution against a routine reliance on post-hoc gene flow interpretations.

Particle Captures and the Method of Suspension Feeding by Echinoderm Larvae

Motivated by discrepancies between two recent descriptions of the suspension-feeding mechanism employed by echinoderm larvae, I describe particle captures by the larvae of seven species of temperate eastern Pacific echinoderms from four classes. When videotape recordings of free-swimming larvae clearing plastic spheres from suspension were analyzed, two modes of particle capture were observed to operate. The majority of captured spheres were caught at the peripheral ciliated band and then transported to the mouth, often by repeated capture on portions of the band progressively nearer to the mouth. This description is consistent with the ciliary reversal model of suspension feeding described by R. R. Strathmann. A small minority of captured spheres followed broad, curving paths directly into the larval mouth without interception at the ciliated band. These particle paths resemble those described by T. H. J. Gilmour. The videotape recordings also permitted a quantitative comparison of suspension feeding by these larvae. Several aspects of this behavior varied among developmental stages or among types of larvae, including: the distribution of particle captures among different segments of the ciliated band, the number of captures for single particles en route to the mouth, and the frequency of particles lost after initial capture. This variation raises a number of questions regarding the feeding performance of different larval species and the efficacy of these different larvae as elements of a reproductive strategy.

Spawning, copulation and inbreeding coefficients in marine invertebrates

Patterns of population genetic variation have frequently been understood as consequences of life history covariates such as dispersal ability and breeding systems (e.g. selfing). For example, marine invertebrates show enormous variation in life history traits that are correlated with the extent of gene flow between populations and the magnitude of differentiation among populations at neutral genetic markers (FST). Here we document an unexpected correlation between marine invertebrate life histories and deviation from Hardy–Weinberg equilibrium (non-zero values of FIS, the inbreeding coefficient). FIS values were significantly higher in studies of species with free-spawned planktonic sperm than in studies of species that copulate or have some form of direct sperm transfer to females or benthic egg masses. This result was robust to several different analytical approaches. We note several mechanisms that might contribute to this pattern, and appeal for more studies and ideas that might help to explain our observations.

Open and closed domains in the mouse genome are configured as 10‐nm chromatin fibres

The mammalian genome is compacted to fit within the confines of the cell nucleus. DNA is wrapped around nucleosomes, forming the classic ‘beads‐on‐a‐string’ 10‐nm chromatin fibre. Ten‐nanometre chromatin fibres are thought to condense into 30‐nm fibres. This structural reorganization is widely assumed to correspond to transitions between active and repressed chromatin, thereby representing a chief regulatory event. Here, by combining electron spectroscopic imaging with tomography, three‐dimensional images are generated, revealing that both open and closed chromatin domains in mouse somatic cells comprise 10‐nm fibres. These findings indicate that the 30‐nm chromatin model does not reflect the true regulatory structure in vivo.

COLONIZATION, DISPERSAL, AND HYBRIDIZATION INFLUENCE PHYLOGEOGRAPHY OF NORTH ATLANTIC SEA URCHINS (STRONGYLOCENTROTUS DROEBACHIENSIS)

Abstract We used frequency‐based and coalescent‐based phylogeographic analysis of sea urchin (Strongylocentrotus droebachiensis) mitochondrial DNA (mtDNA) sequences and previously published microsatellite data to understand the relative influence of colonization and gene flow from older (north Pacific) and younger (northeast Atlantic) sea urchin populations on genetic variation in the northwest Atlantic. We found strong evidence of survival of northwestern Atlantic populations in local Pleistocene glacial refugia: most haplotypes were the same as or closely related to Pacific haplotypes, with deep gene genealogies that reflect divergence times within the northwestern Atlantic that are much older than the last glacial maximum. We detected gene flow across the North Atlantic in the form of haplotypes shared with or recently descended from European populations. We also found evidence of significant introgression of haplotypes from a closely related species (S. pallidus). The relative magnitude of gene flow estimated by coalescent methods (and the effective population size differences among oceanic regions) depended on the genetic marker used. In general, we found very small effective population size in the northeastern Atlantic and high trans‐Arctic gene flow between the Pacific and northwestern Atlantic. Both analyses suggested significant back‐migration to the Pacific. However, microsatellites more strongly reflected older Pacific migration (with similar effective population sizes across the Arctic), whereas mtDNA sequences appeared to be more sensitive to recent trans‐ Atlantic dispersal (with larger differences in effective population size). These differences across marker types might have several biological or methodological causes, and they suggest caution in interpretation of the results from a single locus or class of markers.

EVOLUTIONARY LOSS OF LARVAL FEEDING: DEVELOPMENT, FORM AND FUNCTION IN A FACULTATIVELY FEEDING LARVA, BRISASTER LATIFRONS

Species with large eggs and nonfeeding larvae have evolved many times from ancestors with smaller eggs and feeding larvae in numerous groups of aquatic invertebrates and amphibians. This change in reproductive allocation and larval form is often accompanied by dramatic changes in development. Little is known of this transformation because the intermediate form (a facultatively feeding larva) is rare. Knowledge of facultatively feeding larvae may help explain the conditions under which nonfeeding larvae evolve. Two hypotheses concerning the evolutionary loss of larval feeding are as follows: (1) large eggs evolve before modifications in larval development, and (2) the intermediate form (facultatively feeding larva) is evolutionarily short‐lived. I show that larvae of a heart urchin, Brisaster latifrons, are capable of feeding but do not require food to complete larval development. Food for larvae appears to have little effect on larval growth and development. The development, form, and suspension feeding mechanism of these larvae are similar to those of obligate‐feeding larvae of other echinoids. Feeding rates of Brisaster larvae are similar to cooccurring, obligate‐feeding echinoid larvae but are low relative to the large size of Brisaster larvae. The comparison shows that in Brisaster large egg size, independence from larval food, and relatively low feeding rate have evolved before the heterochronies and modified developmental mechanisms common in nonfeeding echinoid larvae. If it is general, the result suggests that hypotheses concerning the origin of nonfeeding larval development should be based on ecological factors that affect natural selection for large eggs, rather than on the evolution of heterochronies and developmental novelties in particular clades. I also discuss alternative hypotheses concerning the evolutionary persistence of facultative larval feeding as a reproductive strategy. These hypotheses could be tested against a phylogenetic hypothesis.