Can simple population genetic models reconcile partial match frequencies observed in large forensic databases?

A recent study of partial matches in the Arizona offender database of DNA profiles has revealed a large number of nine and ten locus matches. I use simple models that incorporate the product rule, population substructure, and relatedness to predict the expected number of matches in large databases. I find that there is a relatively narrow window of parameter values that can plausibly describe the Arizona results. Further research could help determine if the Arizona samples are congruent with some of the models presented here or whether fundamental assumptions for predicting these match frequencies requires adjustments.     

How is diversity related to species turnover through time?

Empirical studies across a wide range of taxa show that the slopes of species–time relationships often decline as average species richness increases, indicating that more diverse communities have greater temporal stability in species composition. I explored potential explanations for this observation using two simple model formulations for species temporal dynamics. In the Abiotic model, species turnover is governed by the degree of heterogeneity in the environment and the range of species' tolerances. In this case, more variable conditions lead to lower species richness and higher turnover, but only if the distribution of species' niche widths and the size of the species pool are independent of the degree of environmental variability. The Biotic model represents direct effects of diversity on turnover through positive or negative feedbacks between diversity and species' colonization and extinction rates. Declining turnover with increasing richness occurred when higher diversity either facilitated colonization by new species or reduced extinction rates of extant species. Both models could produce the observed pattern of declining turnover at higher diversity under some circumstances, however the conditions for this outcome in the Abiotic model were restrictive and potentially unrealistic. The models provide a process-based framework for understanding the connection between diversity and species turnover through time.     

What is a species? Essences and generation

Arguments against essentialism in biology rely strongly on a claim that modern biology abandoned Aristotle’s notion of a species as a class of necessary and sufficient properties. However, neither his theory of essentialism, nor his logical definition of species and genus (eidos and genos) play much of a role in biological research and taxonomy, including his own. The objections to natural kinds thinking by early twentieth century biologists wrestling with the new genetics overlooked the fact that species have typical developmental cycles and most have a large shared genetic component. These are the “what-it-is-to-be” members of that species. An intrinsic biological essentialism does not commit us to Aristotelian notions, nor even modern notions, of essence. There is a long-standing definition of “species” and its precursor notions that goes back to the Greeks, and which Darwin and pretty well all biologists since him share, that I call the Generative Conception of Species. It relies on there being a shared generative power that makes progeny resemble parents. The “what-it-is-to-be” a member of that species is that developmental type, mistakes in development notwithstanding. Moreover, such “essences” have always been understood to include deviations from the type. Finally, I shall examine some implications of the collapse of the narrative about essences in biology.     

How much is a lot? Seed dispersal by white-faced capuchins and implications for disperser-based studies of seed dispersal systems

The quantity of seeds dispersed is considered one of several means to determine the dispersal effectiveness of an animal. However, there is little consistency in the manner in which quantities are measured or presented. Here, we quantify seed dispersal by white-faced capuchin monkeys (Cebus capucinus) in Santa Rosa National Park, Costa Rica by measuring: degree of frugivory, number of plant species consumed, the number of seeds consumed per unit time, the number of seeds dispersed intact per unit time, and the number of seeds dispersed intact per unit space. Forty-nine percent of C. capucinus diet is composed of the fruit of 39 species, 4 of which constitute 82% of the frugivory. Seventy-four percent of consumed fruits contain seeds that pass intact through the capuchin digestive system. Capuchins pass a mean of 15.7 seeds of a mean of 1.3 species per defecation, and defecate 25.4 times per 12-h day. These numbers are compared with extant data for C. capucinus, and possible reasons for discrepancies among results between studies are discussed. We propose a standardization of quantitative measures of seed dispersal so that quantifications of seed dispersal can be compared within species, and eventually across species.     

How is a seita fitted to the body?

A seita is a carrier frame for backpacking used in Nishiki-cho, Yamaguchi Prefecture, Japan. In this mountainous district, people make their living by agriculture and forestry and carry everything on their backs with seita. In this study, we investigated the relationships between the sizes of a body and the dimensions of a seita. This survey was conducted on 30 subjects (mean +/- SD; 68.1 +/- 9.0 years old) at three mountain villages. We measured some anthropometric sizes and seita dimensions and found that the correlation between height and sum of shoulder-lumbar-nuki distance (back length of a seita) and shoulder strap length is significant. In additional surveys, we took photographs with some markers on iliocristale, trochanterion, and so on, when the subjects carried seita in two load conditions. The photographs indicate that the load-supporting points in 16 of 23 subjects were between the iliocristale and trochanterion (i.e., on the sacrum). It is important to note that nobody showed that point above the iliocristale (i.e., on the lumbar vertebra). These data lead to the conclusion that when people in Nishik-icho carry loads with seita, they support loads not on the lumbar vertebrae but on the sacrum, and that they adjust the perimeter consisting of the back part and shoulder strap of the seita.     

How do we decide that a species is sex-role reversed?

Defining sex roles has been driven by differences in mating systems at the extreme: polygyny and polyandry. Roles may reverse depending on which sex limits the reproductive rate of the other, and it is generally the female that limits the male. Males therefore compete for female mates. But in species in which the male limits the reproductive rate of the female, the female competes for male mates and assumes the masculine role. Complications arise, however, in species with typical roles when males are temporarily limiting, and females then briefly compete for and display to males. Problems also occur among tightly monogamous species with biparental care, where the mates have equal reproductive rates; both males and females compete intrasexually for mates. Despite this, monogamous species have masculine and feminine roles, typically manifested as the male dominating the female. Some monogamous species are nevertheless sex-role reversed. The pervasive behavioral mechanism characterizing the masculine role is dominance through aggression, size, or both. Attending more to behavioral mechanisms will enrich our understanding of sex-role reversal.     

How is extinction risk related to population-size variability over time? A family of models for species with repeated extinction and immigration

It is well known that for an isolated population, the probability of extinction is positively related to population size variation: more variation is associated with more extinction. What, then, is the relation of extinction to population size variation for a population embedded in a metapopulation and subjected to repeated extinction and recolonization? In this case, the extinction risk can be measured by the extinction rate, the frequency at which local extinction occurs. Using several population dynamics models with immigration, we find, in general, a negative correlation between extinction and variation. More precisely, with increasing length of the time series, an initially negative regression coefficient first becomes more negative, then becomes less negative, and eventually attains positive values before decreasing again to 0. This pattern holds under substantial variation in values of parameters representing species and environmental properties. It is also rather robust to census interval length and the fraction of missed individuals but fails to hold for high thresholds (population size values below which extinction is deemed to occur) when quasi extinction rather than true extinction is represented. The few departures from the initial negative correlation correspond to populations at risk: low growth rate or frequent catastrophes.     

How to lift a model for individual behaviour to the population level?

The quick answer to the title question is: by bookkeeping; introduce as p(opulation)-state a measure telling how the individuals are distributed over their common i(ndividual)-state space, and track how the various i-processes change this measure. Unfortunately, this answer leads to a mathematical theory that is technically complicated as well as immature. Alternatively, one may describe a population in terms of the history of the population birth rate together with the history of any environmental variables affecting i-state changes, reproduction and survival. Thus, a population model leads to delay equations. This delay formulation corresponds to a restriction of the p-dynamics to a forward invariant attracting set, so that no information is lost that is relevant for long-term dynamics. For such equations there exists a well-developed theory. In particular, numerical bifurcation tools work essentially the same as for ordinary differential equations. However, the available tools still need considerable adaptation before they can be practically applied to the dynamic energy budget (DEB) model. For the time being we recommend simplifying the i-dynamics before embarking on a systematic mathematical exploration of the associated p-behaviour. The long-term aim is to extend the tools, with the DEB model as a relevant goal post.     

How do low dispersal species establish large range sizes? The case of the water beetle Graphoderus bilineatus

Species’ dispersal abilities have been considered a major driving force in establishment and maintenance of large range sizes. However, recent studies question the general validity of this relationship because the relationship between dispersal ability and range size might in some cases be less important than species phylogeny or local spatial attributes. In this study we used the water beetle Graphoderus bilineatus a philopatric species of conservation concern in Europe as a model to explain large range size and to support effective conservation measures for such species that also have limited dispersal. We recorded the presence/absence of G. bilineatus and measured 14 habitat and 20 landscape variables at 228 localities in Estonia, Poland and Sweden within the core range of the species. Using information theory and average multivariate logistic regression models we determined that presence of G. bilineatus depended on landscape connectivity, distance to a possible source habitat, and stability of the site; however, specificity of habitat characteristics was not vital for the species. We reason that the large range of G. bilineatus is best explained by the historical combination of lakes, river systems and wetlands which used to be highly connected throughout the central plains of Europe. Our data suggest that a broad habitat niche can prevent landscape elements from becoming barriers for species like G. bilineatus. Therefore, we question the usefulness of site protection as conservation measures for G. bilineatus and similar philopatric species. Instead, conservation actions should be focused at the landscape level to ensure a long‐term viability of such species across their range.     

How normal is a "normal" flora in animal or man?

When investigating different disturbances of the normal intestinal flora causing disorders and/or diseases in man and animal, these studies include comparisons of results with control materials, i.e., materials from conventional laboratory animals or healthy human beings. However, how "normal" is the control group’s flora? In this paper two different examples will be discussed; one investigation with laboratory animals and one from a human study.     

How are tree species distributed in climatic space? A simple and general pattern

Aim Although many factors undoubtedly affect species geographic distributions, can a single, simple model nonetheless capture most of the spatial variation in the probability of presence/absence in a large set of species? For 482 North American tree species that occur east of the Rocky Mountains, we investigated the shape(s) of the relationship between the probability of occupancy of a given location and macroclimate, and its consistency among species and regions. Location North America. Methods Using Little's tree range maps, we tested four hypothetical shapes of response relating occupancy to climate: (1) high occupancy of all suitable climates; (2) threshold response (i.e. unsuitable climates exclude species, but within the thresholds, species presence is independent of climate); (3) occupancy is a bivariate normal function of annual temperature and precipitation; and (4) asymmetric limitation (i.e. abiotic factors set abrupt range limits in stressful climates only). Finally, we compared observed climatic niches with the occupancy of similar climates on off‐shore islands as well as west of the Rockies. Results (a) Species' distributions in climatic space do not have strong thresholds, nor are they systematically skewed towards less stressful climates. (b) Occupancy can generally be described by a bivariate normal function of temperature and precipitation, with little or no interaction between the two variables. This model, averaged over all species, accounts for 82% of the spatial variation in the probability of occupancy of a given area. (c) Occupied geographic ranges are typically ringed by unoccupied, but climatically suitable areas. (d) Observed climatic niche positions are largely conserved between regions. Main conclusions We conclude that, despite the complexities of species histories and biologies, to a first approximation most of the variation in their geographic distributions relates to climate, in similar ways for nearly all species.     

Salt and water balance in the sipunculan phascolopsis gouldi: is any animal a “simple osmometer”?

• 1.1. Phascolopsis gouldi, the commonly studied sipunculan of the Woods Hole area, Massachusetts, can tolerate a salinity range from about 45% seawater to at least 100% SW, with literature records extending to about 160% SW. There was no survival at 40% SW.
• 2.2. Over this salinity range, P. gouldi is an osmotic and ionic conformer.
• 3.3. The osmotic and sodium concentrations of the coelomic fluid are the same as that of the medium; the chloride concentration is about 9% less than that of the medium; the potassium concentration is about 30% higher.
• 4.4. Analysis of water content regulation by two different approaches shows that P. gouldi does have a limited ability for volume regulation, restricted to salinities higher than 58% SW.
• 5.5. P. gouldi is not a “simple osmometer”.

     

How intellectual is chess? -- a reply to Howard

Howard's (2005) claim that male dominance in chess is 'consistent with the evolutionary psychology view that males predominate at high achievement levels at least partly because of ability differences' (p. 378) is based on the premise that top level chess skill depends on a high level of IQ and visuospatial abilities. This premise is not supported by empirical evidence. In 1927 Djakow et al. first showed that world-class chess players do not have exceptional intellectual abilities. This finding has subsequently been confirmed many times. Different participation rates, or differences in the amount of practice, motivation and interest for chess in male and female chess players, may provide a better explanation for gender differences in chess performance.     

Using Africa's protected area network to estimate the global population of a threatened and declining species: a case study of the Critically Endangered White‐headed Vulture Trigonoceps occipitalis

The White‐headed Vulture Trigonoceps occipitalis (WhV) is uncommon and largely restricted to protected areas across its range in sub‐Saharan Africa. We used the World Database on Protected Areas to identify protected areas (PAs) likely to contain White‐headed Vultures. Vulture occurrence on road transects in Southern, East, and West Africa was adjusted to nests per km² using data from areas with known numbers of nests and corresponding road transect data. Nest density was used to calculate the number of WhV nests within identified PAs and from there extrapolated to estimate the global population. Across a fragmented range, 400 PAs are estimated to contain 1893 WhV nests. Eastern Africa is estimated to contain 721 nests, Central Africa 548 nests, Southern Africa 468 nests, and West Africa 156 nests. Including immature and nonbreeding birds, and accounting for data deficient PAs, the estimated global population is 5475 ‐ 5493 birds. The identified distribution highlights are alarming: over 78% (n = 313) of identified PAs contain fewer than five nests. A further 17% (n = 68) of PAs contain 5 ‐ 20 nests and 4% (n = 14) of identified PAs are estimated to contain >20 nests. Just 1% (n = 5) of PAs are estimated to contain >40 nests; none is located in West Africa. Whilst ranging behavior of WhVs is currently unknown, 35% of PAs large enough to hold >20 nests are isolated by more than 100 km from other PAs. Spatially discrete and unpredictable mortality events such as poisoning pose major threats to small localized vulture populations and will accelerate ongoing local extinctions. Apart from reducing the threat of poisoning events, conservation actions promoting linkages between protected areas should be pursued. Identifying potential areas for assisted re‐establishment via translocation offers the potential to expand the range of this species and alleviate risk.     

How do invasive species travel to and through urban environments?

Globalisation has resulted in the movement of organisms outside their natural range, often with negative ecological and economic consequences. As cities are hubs of anthropogenic activities, with both highly transformed and disturbed environments, these areas are often the first point of entry for alien species. We compiled a global database of cities with more than one million inhabitants that data had on alien species occurrence. We then identified the most prominent pathways of introduction and vectors of spread of alien species in these cities. Most species were intentionally introduced to cities and were released or escaped from confinement. The majority of alien species then spread within cities through natural means (primarily unaided dispersal). Pathway prominence varied across the taxonomic groups of alien species: the most prominent pathway for plants and vertebrates was the escape pathway; for invertebrates the stowaway and contaminant pathways were most likely to facilitate introductions. For some organisms, pathway prominence varied with the geographical and climatic characteristics of the city. The characteristics of the cities also influenced the prominence of vectors of spread for alien species. Preventing the natural spread of alien species within cities, and into adjacent natural environments will be, at best, difficult. To prevent invasions, both the intentional and unintentional introduction of potentially harmful alien species to cities must be prevented. The pathways of introduction and vectors of spread identified here should be prioritised for management.