Steven C. Le Comber

Next Generation Sequencing Reveals Genome Downsizing in Allotetraploid Nicotiana tabacum, Predominantly through the Elimination of Paternally Derived Repetitive DNAs

We used next generation sequencing to characterize and compare the genomes of the recently derived allotetraploid, Nicotiana tabacum (<200,000 years old), with its diploid progenitors, Nicotiana sylvestris (maternal, S-genome donor), and Nicotiana tomentosiformis (paternal, T-genome donor). Analysis of 14,634 repetitive DNA sequences in the genomes of the progenitor species and N. tabacum reveal all major types of retroelements found in angiosperms (genome proportions range between 17-22.5% and 2.3-3.5% for Ty3-gypsy elements and Ty1-copia elements, respectively). The diploid N. sylvestris genome exhibits evidence of recent bursts of sequence amplification and/or homogenization, whereas the genome of N. tomentosiformis lacks this signature and has considerably fewer homogenous repeats. In the derived allotetraploid N. tabacum, there is evidence of genome downsizing and sequences loss across most repeat types. This is particularly evident amongst the Ty3-gypsy retroelements in which all families identified are underrepresented in N. tabacum, as is 35S ribosomal DNA. Analysis of all repetitive DNA sequences indicates the T-genome of N. tabacum has experienced greater sequence loss than the S-genome, revealing preferential loss of paternally derived repetitive DNAs at a genome-wide level. Thus, the three genomes of N. sylvestris, N. tomentosiformis, and N. tabacum have experienced different evolutionary trajectories, with genomes that are dynamic, stable, and downsized, respectively.

Mate fidelity and intra-lineage polygyny in greater horseshoe bats

Mating strategies that lead to increased kinship within socially cooperative groups may offer inclusive fitness benefits to individuals, but can also result in higher levels of inbreeding. Here we show in a sexually segregated bat species that females avoid this conflict through two mating behaviours. First, most females revisit and breed with specific, individual males across years, so that their single offspring born in different years are full siblings. Second, relatives in the maternal line, including mothers and daughters, share breeding partners (intra-lineage polygyny) more often than expected by chance. Although these behaviours increased levels of co-ancestry among colony members, there was no concomitant rise in inbreeding. We suggest that when females engage in mate fidelity and intra-lineage polygyny, kin ties among female roost mates will be strengthened, thereby potentially contributing to social group cohesiveness. Our findings reveal the hidden complexity that can underlie polygynous breeding, and highlight a new potential route by which female mate choice could influence social evolution.

Bees do not use nearest-neighbour rules for optimization of multi-location routes.

Animals collecting patchily distributed resources are faced with complex multi-location routing problems. Rather than comparing all possible routes, they often find reasonably short solutions by simply moving to the nearest unvisited resources when foraging. Here, we report the travel optimization performance of bumble-bees (Bombus terrestris) foraging in a flight cage containing six artificial flowers arranged such that movements between nearest-neighbour locations would lead to a long suboptimal route. After extensive training (80 foraging bouts and at least 640 flower visits), bees reduced their flight distances and prioritized shortest possible routes, while almost never following nearest-neighbour solutions. We discuss possible strategies used during the establishment of stable multi-location routes (or traplines), and how these could allow bees and other animals to solve complex routing problems through experience, without necessarily requiring a sophisticated cognitive representation of space.

Geographic profiling applied to testing models of bumble-bee foraging

Geographic profiling (GP) was originally developed as a statistical tool to help police forces prioritize lists of suspects in investigations of serial crimes. GP uses the location of related crime sites to make inferences about where the offender is most likely to live, and has been extremely successful in criminology. Here, we show how GP is applicable to experimental studies of animal foraging, using the bumble-bee Bombus terrestris. GP techniques enable us to simplify complex patterns of spatial data down to a small number of parameters (2–3) for rigorous hypothesis testing. Combining computer model simulations and experimental observation of foraging bumble-bees, we demonstrate that GP can be used to discriminate between foraging patterns resulting from (i) different hypothetical foraging algorithms and (ii) different food item (flower) densities. We also demonstrate that combining experimental and simulated data can be used to elucidate animal foraging strategies: specifically that the foraging patterns of real bumble-bees can be reliably discriminated from three out of nine hypothetical foraging algorithms. We suggest that experimental systems, like foraging bees, could be used to test and refine GP model predictions, and that GP offers a useful technique to analyse spatial animal behaviour data in both the laboratory and field.

Flow cytometry and GISH reveal mixed ploidy populations and Spartina nonaploids with genomes of S. alterniflora and S. maritima origin

BACKGROUND The genus Spartina exhibits extensive hybridization and includes classic examples of recent speciation by allopolyploidy. In the UK there are two hexaploid species, S. maritima and S. alterniflora, as well as the homoploid hybrid S. x townsendii (2n = 60) and a derived allododecaploid S. anglica (2n = 120, 122, 124); the latter two are considered to have originated in Hythe, southern England at the end of the 19th century. METHODS Genomic in situ hybridization (GISH) and flow cytometry were used to characterize the genomic composition and distribution of these species and their ploidy levels at Eling Marchwood and Hythe, both near Southampton, southern England. KEY RESULTS GISH identified approx. 60 chromosomes each of S. maritima and S. alterniflora origin in S. anglica and 62 chromosomes from S. alterniflora and 30 chromosomes from S. maritima in a nonaploid individual from Eling Marchwood, UK. GISH and flow cytometry also revealed that most (94 %) individuals examined at Hythe were hexaploid (the remaining two individuals (6 %) were dodedcaploid; n = 34), whereas hexaploid (approx. 36 % of plants), nonaploid (approx. 27 %) and dodecaploid (approx. 36 %) individuals were found at Eling Marchwood (n = 22). CONCLUSIONS Nonaploid individuals indicate the potential for introgression between hexaploid and dodecaploid species, complicating the picture of polyploid-induced speciation within the genus. Despite the aggressive ecological habit of S. anglica, it has not out-competed S. x townsendii at Hythe (homoploid hybrids at a frequency of 94 %, n = 34), despite >100 years of coexistence. The success of GISH opens up the potential for future studies of polyploid-induced genome restructuring in this genus.

On the Occlusal Fit of Tribosphenic Molars: Are We Underestimating Species Diversity in the Mesozoic?

The complex occlusal fits between tribosphenic teeth are a rich source of information for taxonomic, phylogenetic, and evolutionary analysis. The degree of fit between upper and lower cheek teeth has been used to refer specimens to species-level taxa, but statistical data on occlusal fit in relation to taxonomic identity have been lacking. We used landmarks on upper and lower first molars of 20 bat populations representing 16 species to assess the degree of occlusal fit (1) between teeth from the same individual; (2) between teeth from different individuals belonging to the same populations; and (3) between teeth belonging to different populations. We found that the fit of teeth belonging to different populations was significantly worse than between those of the same population and that the degree of misfit increased linearly with time since common ancestry, albeit with substantial variance. We used our comparisons to assess the species-level diversity within Batodon, the smallest known placental mammal from the Cretaceous. Our data suggest, with caveats, that instead of belonging to a single species, the specimens assigned to Batodon represent at least two species as different as those belonging to different genera or families of living bats.

Measures of pocket gopher ( Thomomys bottae ) burrow geometry: correlates of fractal dimension

For many burrowing species of mammals, the shape of the burrow may affect the success with which resources are acquired. Parameters used to characterize burrows have included: number of branches, mean segment length, turn angle, and linearity. However, the interactions among these parameters are unclear, making it desirable to find a single measure to characterize burrow geometry. For this reason, fractal dimension has been proposed as a measure of burrow geometry. However, the ways in which fractal dimension relates to other burrow metrics are not obvious. In this study, we examine correlations between fractal dimension and other measures of burrow geometry, using burrows of the pocket gopher Thomomys bottae. We also investigate whether burrows excavated by pocket gophers of different age, sex, and at two locations differing in food abundance have different fractal dimensions. We show that there are strong correlations between fractal dimension and other measures of burrow geometry, but that replacing fractal dimension with any single measure of burrow geometry discards important information about burrow structure. We conclude that fractal dimension offers a useful way of describing burrow geometry. No differences were found in burrow fractal dimension between pocket gophers of different ages or sex or in sites of different productivities, and we conclude that the factors that determine the pattern of burrowing in this species are invariant with respect to these parameters.

Response of territorial males to the threat of sneaking in the three‐spined stickleback (Gasterosteus aculeatus): a field study

Alternative mating tactics are found in many species, and may have important implications for population genetics and speciation. The existence of such alternative mating tactics is well-documented in the three-spined stickleback Gasterosteus aculeatus , and sneaking and egg-stealing may occur in a significant proportion of matings under natural conditions. Sneaking can impose high costs on territorial males, both in terms of reduced reproductive output and caring for unrelated offspring. We ask whether territorial males adjust their behaviour in response to the risk of sneaking. In a field study of three-spined sticklebacks on the Isle of Arran, Scotland, territorial males were presented with glass bottles containing either a male, a female or neither, to address whether territorial males were more aggressive to other males in the presence of a female, and whether territorial males courted females less in the presence of another male. Behavioural observations showed that territorial males did not behave more aggressively towards rival males in the presence of a female, but did reduce their rate of courtship towards females in the presence of rival males. We conclude that territorial males adopt behavioural strategies that may reduce their risk of reproductive parasitism.

Flower color phenology in European grassland and woodland habitats, through the eyes of pollinators

Some studies have claimed that flowers in bloom at particular times of year are more likely to be of particular colors to better attract pollinating insects. To test this, we analyzed a data set collected from five field sites near Strausberg, Germany, which included information on flower color and months of blooming. However, we chose to consider flower color as perceived by bee as well as human visual systems, as well as independent of any color vision system, to reveal whether trends, if present, have any ecological relevance. Using randomization analyses, we were able to consider whether blooming time interacts with flower color, and how this interaction depends upon other factors. Our results show that there is an association between the months of flowering and the colors of flowers — but only when flowers are considered according to human color categories. Further analysis showed that this is merely a consequence of flowers from the same family being more likely to flower at the same time and have similar colors. All these effects disappeared when flowers were considered using bee color categories, and in the analyses of physical spectral reflectances.

Spatial methods for infectious disease outbreak investigations: systematic literature review.

Investigations of infectious disease outbreaks are conventionally framed in terms of person, time and place. Although geographic information systems have increased the range of tools available, spatial analyses are used relatively infrequently. We conducted a systematic review of published reports of outbreak investigations worldwide to estimate the prevalence of spatial methods, describe the techniques applied and explore their utility. We identified 80 reports using spatial methods published between 1979 and 2013, ca 0.4% of the total number of published outbreaks. Environmental or waterborne infections were the most commonly investigated, and most reports were from the United Kingdom. A range of techniques were used, including simple dot maps, cluster analyses and modelling approaches. Spatial tools were usefully applied throughout investigations, from initial confirmation of the outbreak to describing and analysing cases and communicating findings. They provided valuable insights that led to public health actions, but there is scope for much wider implementation and development of new methods.