Deciphering past human population movements in Oceania: provably optimal trees of 127 mtDNA genomes

The settlement of the many island groups of Remote Oceania occurred relatively late in prehistory, beginning approximately 3,000 years ago when people sailed eastwards into the Pacific from Near Oceania, where evidence of human settlement dates from as early as 40,000 years ago. Archeological and linguistic analyses have suggested the settlers of Remote Oceania had ancestry in Taiwan, as descendants of a proposed Neolithic expansion that began approximately 5,500 years ago. Other researchers have suggested that the settlers were descendants of peoples from Island Southeast Asia or the existing inhabitants of Near Oceania alone. To explore patterns of maternal descent in Oceania, we have assembled and analyzed a data set of 137 mitochondrial DNA (mtDNA) genomes from Oceania, Australia, Island Southeast Asia, and Taiwan that includes 19 sequences generated for this project. Using the MinMax Squeeze Approach (MMS), we report the consensus network of 165 most parsimonious trees for the Oceanic data set, increasing by many orders of magnitude the numbers of trees for which a provable minimal solution has been found. The new mtDNA sequences highlight the limitations of partial sequencing for assigning sequences to haplogroups and dating recent divergence events. The provably optimal trees found for the entire mtDNA sequences using the MMS method provide a reliable and robust framework for the interpretation of evolutionary relationships and confirm that the female settlers of Remote Oceania descended from both the existing inhabitants of Near Oceania and more recent migrants into the region.     

Density-dependent population dynamics in clonal organisms: a modelling approach

1. Density dependence may act at several stages in an organisms life-cycle (e.g. on mortality, fecundity, etc.), but not all density-dependent processes necessarily regulate population size. In this paper I use a density manipulation experiment to determine the effects of density on the transition rates between different size classes of the clonal zoanthid Palythoa caesia Dana 1846. I then formulate a density-dependent matrix model of population dynamics of Palythoa , and perform a series of sensitivity analyses on the model to determine at what stage in the life-cycle regulation acts.
2. Seven of the 16 transition probabilities decreased with density, most of them being shrinkage (due to loss of tissue or fission) and stasis (the self–self transition) of medium and large colonies. The only probability to increase was for the stasis of large colonies. Recruitment was quadratically dependent on density, peaking at intermediate densities.
3. Equilibrium cover in the model was 84% and was reached in ≈40 years. To determine which density-dependent transitions were involved in population regulation, the strength of density dependence was varied in each independently. This sensitivity analysis showed that only changes in the probabilities of large colonies remaining large and producing medium colonies, were regulating.
4. These results suggest that regulation is primarily acting on fission of large colonies to produce intermediate-sized colonies, in combination with size specific growth rates. Fission rates decrease greatly with density, resulting in a greater proportion of large colonies at high densities and large colonies grow more slowly than small. Overall, this behaviour is very similar to that of clonal plants which have a phalanx type life history.     

Rainfall and rats: Climatically-driven dynamics of a tropical rodent population

A five-year mark–recapture study of dusky rats (Rattus colletti) on the Adelaide River floodplain, within the Australian wet–dry tropics, revealed substantial spatial and temporal variation in demographic characteristics (abundance, condition, and rates of survival, growth, and reproduction) of the rats. Our data suggest that annual variation in the intensity and timing of monsoonal rainfall during the ‘wet-season’ is the main factor driving the demography of the rats. When total rainfall figures are modified to reflect the magnitude and duration of inundation of the floodplain each year, a link is evident between rainfall patterns and the rat population dynamics. Minor spatial variations in elevation (and hence, in the duration of inundation) across the floodplain engender large differences in rat growth rates, condition factors, survival rates, and the duration of reproductive activity each year. Because these rats have very high reproductive rates, small rain-induced differences in the duration of their reproductive season (i.e. number of litters per year) can cause massive differences in subsequent rat abundances. Hence, rat numbers can be predicted from rainfall patterns during the preceding wet-season. Similar links between rainfall, the duration of breeding, and fluctuations in abundance may typify many rodent populations in tropical and arid regions of the world.     

Contrasting signatures of population growth for mitochondrial DNA and Y chromosomes among human populations in Africa

A history of Pleistocene population expansion has been inferred from the frequency spectrum of polymorphism in the mitochondrial DNA (mtDNA) of many human populations. Similar patterns are not typically observed for autosomal and X-linked loci. One explanation for this discrepancy is a recent population bottleneck, with different rates of recovery for haploid and autosomal loci as a result of their different effective population sizes. This hypothesis predicts that mitochondrial and Y chromosomal DNA will show a similar skew in the frequency spectrum in populations that have experienced a recent increase in effective population size. We test this hypothesis by resequencing 6.6 kb of noncoding Y chromosomal DNA and 780 basepairs of the mtDNA cytochrome c oxidase subunit III (COIII) gene in 172 males from 5 African populations. Four tests of population expansion are employed for each locus in each population: Fu's Fs statistic, the R(2) statistic, coalescent simulations, and the mismatch distribution. Consistent with previous results, patterns of mtDNA polymorphism better fit a model of constant population size for food-gathering populations and a model of population expansion for food-producing populations. In contrast, none of the tests reveal evidence of Y chromosome growth for either food-gatherers or food-producers. The distinct mtDNA and Y chromosome polymorphism patterns most likely reflect sex-biased demographic processes in the recent history of African populations. We hypothesize that males experienced smaller effective population sizes and/or lower rates of migration during the Bantu expansion, which occurred over the last 5,000 years.     

Circadian analysis of large human populations: Inferences from the power grid

Few, if any studies have focused on the daily rhythmic nature of modern industrialized populations. The present study utilized real-time load data from the U.S. Pacific Northwest electrical power grid as a reflection of human operative household activity. This approach involved actigraphic analyses of continuously streaming internet data (provided in 5?min bins) from a human subject pool of approximately 43 million primarily residential users. Rhythm analyses reveal striking seasonal and intra-week differences in human activity patterns, largely devoid of manufacturing and automated load interference. Length of the diurnal activity period (alpha) is longer during the spring than the summer (16.64?h versus 15.98?h, respectively; p?<?0.01). As expected, significantly more activity occurs in the solar dark phase during the winter than during the summer (6.29?h versus 2.03?h, respectively; p?<?0.01). Interestingly, throughout the year a “weekend effect” is evident, where morning activity onset occurs approximately 1?h later than during the work week (5:54 am versus 6:52 am, respectively; p?<?0.01). This indicates a general phase-delaying response to the absence of job-related or other weekday morning arousal cues, substantiating a preference or need to sleep longer on weekends. Finally, a shift in onset time can be seen during the transition to Day Light Saving Time, but not the transition back to Standard Time. The use of grid power load as a means for human actimetry assessment thus offers new insights into the collective diurnal activity patterns of large human populations.     

Image analysis of Daphnia populations: non-destructive determination of demography and biomass in cultures

SUMMARY 1. An image analysis technique was developed for the semiautomatic determination of abundance, size distribution and biomass in Daphnia cultures. This allowed detailed observations of growth, demography and biomass accumulation in live populations, avoiding artifacts caused by subsampling and sampling losses.
2. The image analysis method gave fast, non-destructive and reliable individual counts, even in cultures with high density and a large fraction of juveniles.
3. In Daphnia , animal width changes with nutritional status and growth within instar, while length changes only at the moult. Thus, estimation of individual biomass using an ellipsoidal model based on animal width gave improved biomass calculations compared to manual counting, sizing, and length : weight regressions.
4. The power of the image analysis technique for assessing population growth and size structure was demonstrated in two 40-day experiments, with Daphnia magna feeding on the green algae Selenastrum capricornutum in a two-stage chemostat system.     

Evolution of reproductive effort in viscous populations: the importance of population dynamics

I present two ecological models for the evolution of reproductive effort in viscous populations with empty sites. In contrast with previous studies, I show that limited dispersal needs not have a positive effect on the evolutionarily stable allocation of resources to fecundity versus survival. Rather, depending on the feedback between the trait and the population dynamics, population viscosity may have no effect or even lead to a decrease in the evolutionarily stable reproductive effort when individuals can degrade their environment during their lifetime. I show that the different evolutionary outcomes can be explained by the asymmetry in the level of kin competition resulting from investing into juveniles or into adults.     

不同水稻生育期对稻粉虱种群动态的影响

本主要研究了不同水稻生育期对稻粉虱Aleurocybotus indicus种群动态的影响。研究结果表明,水稻分蘖期至拔节期最容易受稻粉虱为害,卵孵化率为88．1％,拟蛹的羽化率为82．9％,孵化率和羽化率均高于水稻其它生育期。     

Biology of parasite populations: population dynamics of bothriocephalids (Cestoda-Pseudophyllidea) in teleostean fish

Relationships between sympatric populations of four species of Cestoda belonging to the genus Bothriocephalus ( B. barbarus. B. gregarius, B. funiculus and B. scorpii ) and populations of their respective hosts Scophthalmus rhombus, Pserra maxima, Ciliata mustela and Myoxocephalus scorpius were investigated. The parasites were overdispersed within their host populations. The mean intensities of B. burbarus were 1.59 ( s.d. =0.83) in the Mediterranean (Gulf of Lions) and 1.25 ( s.d. =0.53) in the Atlantic (coasts of Brittany). The mean intensities of B. gregarius were 62.3 ( s.d. =49.7) in the Mediterranean and 14.06 ( s.d. =18.48) in the Atlantic, compared to 1.78 ( s.d. =0.3) for B. funiculus and 21.6 ( s.d. =17.3) for B. scorpii .
The distribution of prevalence of B. gregarius corresponded to a lognormal distribution while those of B. barbatus and B. fwticulus corresponded to negative binomials. No differences in infection could be related to host sex. The parasitization of B. gregariusdepended on host size. In brill, infection by E. barbatus was independent of host size and remained stable after the fish reached 180mm in length. Parasitization of turbot by E. gregarius was lower in young fish (≤110–150 mm) and increased with the host size. Compared to the Atlantic populations of B. gregarius and B. barbatus, the Mediterranean populations were more frequently and intensively infected. The differences in the population dynamics of B. gregarius and B. barbarus would appear to depend on whether or not the life cycle involves a paratenic host.     

The contributions of age and sex to variation in common tern population growth rate

1. The decomposition of population growth rate into contributions from different demographic rates has many applications, ranging from evolutionary biology to conservation and management. Demographic rates with low variance may be pivotal for population persistence, but variable rates can have a dramatic influence on population growth rate. 2. In this study, the mean and variance in population growth rate (lambda) is decomposed into contributions from different ages and demographic rates using prospective and retrospective matrix analyses for male and female components of an increasing common tern (Sterna hirundo) population. 3. Three main results emerged: (1) subadult return was highly influential in prospective and retrospective analyses; (2) different age-classes made different contributions to variation in lambda: older age classes consistently produced offspring whereas young adults performed well only in high quality years; and (3) demographic rate covariation explained a significant proportion of variation in both sexes. A large contribution to lambda did not imply a large contribution to its variation. 4. This decomposition strengthens the argument that the relationship between variation in demographic rates and variation in lambda is complex. Understanding this relationship and its consequences for population persistence and evolutionary change demands closer examination of the lives, and deaths, of the individuals within populations within species.     

An approach to the nonlinear dynamics of Russian wheat aphid population growth with the cusp catastrophe model

Many insect field populations, especially aphids, often exhibit irregular and even catastrophic fluctuations. The objective of the present study is to explore whether or not the population intrinsic rates of growth ( r _m) obtained under laboratory conditions can shed some light on the irregular changes of insect field populations. We propose to use the catastrophe theory, one of the earliest nonlinear dynamics theories, to answer the question. To collect the necessary data, we conducted a laboratory experiment to investigate population growth of the Russian wheat aphid (RWA), Diuraphis noxia (Mordvilko), in growth chambers. The experiment was designed as the factorial combinations of five temperatures and five host plant-growth stages (25 treatments in total): 1800 newly born RWA nymphs arranged in the 25 treatments (each treatment with 72 repetitions) were observed for their development, reproduction and survival through their entire lifetimes. After obtaining the population intrinsic rates of growth ( r _m) from the experimental data under various environmental conditions, we built a cusp catastrophe model for RWA population growth by utilizing r _m as the system state variable, and temperature and host plant-growth stage as control variables. The cusp catastrophe model suggests that RWA population growth is intrinsically catastrophic , and dramatic jumps from one state to another might occur even if the temperature and plant-growth stage change smoothly . Other basic behaviors of the cusp catastrophe model, such as catastrophic jumps , hystersis and divergence , are also expected in RWA populations. These results suggest that the answer to the previously proposed question should be yes.