Climate change and the population collapse during the “Great Famine” in pre‐industrial Europe

Population dynamics, economy, and human demography started with Malthus, the idea that population growth is limited by resources and “positive checks” occur when population growth overshoots the available resources. In fact, historical evidence indicates that long‐term climate changes have destabilized civilizations and caused population collapses via food shortages, diseases, and wars. One of the worst population collapses of human societies occurred during the early fourteenth century in northern Europe; the “Great Famine” was the consequence of the dramatic effects of climate deterioration on human population growth. Thus, part of my motivation was to demonstrate that simple theoretical‐based models can be helpful in understanding the causes of population change in preindustrial societies. Here, the results suggest that a logistic model with temperature as a “lateral” perturbation effect is the key element for explaining the population collapse exhibited by the European population during the “Great Famine”.     

The “Basqueness” of the Basques of Alava: A reappraisal from a multidisciplinary perspective

The genetic and linguistic peculiarity of the Basque population is well known. Analysis of the studies published to date on the Basque population reveals that these studies refer basically to the provinces of Vizcaya and Labourd, both in the Northern part of the Basque Country. Multidisciplinary information indicates that the landscape differences of the Basque Country could have conditioned differential population biodynamics in the Atlantic and Mediterranean parts of the Basque area. In order to evaluate this possibility, this study focuses on the genetic constitution of the Basque population of Alava (in the South of the Basque Country) through the analysis of several red-cell systems. The data obtained in this genetic study and those from archaeology, linguistics, ethnography, and skeletal biology suggest that within the “Basque population” there may be at least two distinct groups: an “Atlantic” group and a “Mediterranean” one, divided mainly by the watershed. This geographical feature could have led to a greater genetic isolation of the Northern slopes, with the South more open to population contact. This is reflected nowadays in the different cline distribution detected for most systems in the Alava Basques in comparison with other Basque and Iberian Peninsula series studied to date. © 1996 Wiley-Liss, Inc.     

Speciation and the “shifting balance” in a continuous population

Shifts between adaptive peaks, caused by sampling drift, are involved in both speciation and adaptation via Wright's “shifting balance.” We use techniques from statistical mechanics to calculate the rate of such transitions for a population in a single panmictic deme and for a population which is continuously distributed over one- and two-dimensional regions. This calculation applies in the limit where transitions are rare. Our results indicate that stochastic divergence is feasible despite free gene flow, provided that neighbourhood size is low enough. In two dimensions, the rate of transition depends primarily on neighbourhood size N and only weakly on selection pressure (≈s^k exp(− cN)), where k is a number determined by the local population structure, in contrast with the exponential dependence on selection pressure in one dimension (≈exp(− cN √s)) or in a single deme (≈exp(− cNs)). Our calculations agree with simulations of a single deme and a one-dimensional population.     

COMPETITION BETWEEN SEGREGATION DISTORTERS: COEXISTENCE OF “SUPERIOR” AND “INFERIOR” HAPLOTYPES AT THE t COMPLEX

By means of population genetical models, we investigate the competition between sex-specific segregation distorters. Although the models are quite general, they are motivated by a specific example, the t complex of the house mouse. Some variants at this gene complex, the t haplotypes, distort Mendelian segregation in heterozygous males in their favor. The selective advantage at the gamete level is counterbalanced by strong negative fitness effects at the individual level (male sterility or even lethality in both sexes). A plethora of different t haplotypes has been found, both in the field and in the lab. Up to now, however, models have focused on the equilibrium frequency of a single t haplotype. In contrast, we explicitly model the competition between several t haplotypes. A deterministic model for a large, well-mixed population predicts a surprisingly high degree of polymorphism. Haplotypes with seemingly inferior fitness characteristics may easily coexist with “superior” haplotypes. For instance, a lethal haplotype with a low segregation ratio may stably coexist with a sterile haplotype with a high segregation ratio. Stable coexistence is even possible for haplotypes with a segregation disadvantage. A simple stochastic model shows that the same principles apply in the context of a structured metapopulation. Although counterintuitive at first sight, all our results can be explained by the fact that segregation distorters have an inherent advantage when they are rare. We conclude that fitness comparisons are not sufficient to predict the outcome of competition when selective forces are acting at different levels.     

Localization of a Mg- or Ca-activated (“basic”) ATPase in skeletal muscle

A chicken pectoralis muscle membrane fraction enriched in a Mg²⁺- or Ca²⁺-activated (‘basic’) ATPase was obtained by sucrose gradient centrifugation. Enzymatic properties of the ‘basic’ ATPase were determined and used to localize its enzymatic activity in situ by ultrastructural cytochemistry. The enzyme was activated by Mg²⁺ or Ca²⁺ but not by Sr²⁺, Ba²⁺, Co²⁺, Ni²⁺ or Pb²⁺. It was present in a membranous fraction with a buoyant density of 1.10-1.12 (24–27.5% (w/w) sucrose). ‘Basic’ ATPase activity had a sedimentation pattern similar to the putative plasma membrane enzymes, 5′-nucleotidase and leucyl β-naphthylamidase, but different from that of sarcoplasmic reticulum Ca²⁺ ATPase. Also unlike sarcoplasmic reticulum Ca²⁺ ATPase, ‘basic’ ATPase was resistant to N-ethylmaleimide and aldehyde fixatives, was active in a medium containing a high Ca²⁺ concentration (3 mM), and was lost when exposed to Triton X-100 or deoxycholate. In cytochemical studies, a low Pb²⁺ concentration was used to capture the enzymatically released phosphate ions. Under conditions which eliminated interfering (Na⁺ + K⁺) ATPase and sarcoplasmic reticulum Ca²⁺ ATPase activities, electron-dense lead precipitates were present at the plasmalemma and T-system membranes. These studies suggest that ‘basic’ ATPase activity is associated with plasmalemma and T-system membranes of skeletal muscle.     

An “omics” approach to bridge community ecology and island biogeography

Understanding the dynamics of communities in space and time requires reconciling ecological and evolutionary processes, including colonization, adaptation, speciation and extinction. In practice, this has been challenging because empirical data obtained by traditional methods and predictive models typically focus on particular processes driving local community assembly and biogeographical structure. In this issue of Molecular Ecology, by using phylogenomics, population genomics and phenomics approaches, Darwell et al. show that ant community assembly on islands is governed by predictable eco‐evolutionary trends of geographical range expansion, adaptive radiation and local population decline. The authors provide one of the most robust lines of evidence that the evolutionary progression of island communities may often be directional and repeatable, as predicted by the concept of taxon cycles.     

FLAT REACTION NORMS AND “FROZEN” PHENOTYPIC VARIATION IN CLONAL SNAILS (POTAMOPYRGUS ANTIPODARUM)

The Frozen Niche-Variation hypothesis (FNV) suggests that clones randomly sample and “freeze” the genotypes of their ancestral sexual populations. Hence, each clone expresses only a fraction of the total niche-use variation observed in the sexual population, which may lead to selection for ecological specialization and coexistence of clones. A generalized form of the FNV model suggests that the same is true for life-history (as well as other) traits that have important fitness consequences, but do not relate directly to niche use. We refer to the general form of the model as the Frozen Phenotypic Variation (FPV) model. A mixed population of sexual and parthenogenetic snails (Potamopyrgus antipodarum) in a New Zealand lake allowed us to examine the phenotypic variation expressed by coexisting clones in two benthic habitats, and to compare that variation to the sexual population. Three clones were found primarily in an aquatic macrophyte zone composed of Isoetes kirkii (1.5–3.0 m deep), and three additional clones were found in a deeper macrophyte zone composed of Elodea canadensis (4.0–6.0 m deep). These clones showed significant variation between habitats, which mirrored that observed in the sexual population. Specifically, clones and sexuals from the deeper habitat matured at a larger size and had larger broods. There was also significant among-clone variation within habitats; and as expected under the FPV model, the within-clone coefficients of variation for size at maturity were low in both habitats when compared to the sexual population. In addition, we found four clones that were common in both macrophyte zones. The reaction norms of these clones were flat across habitats, suggesting little phenotypic plasticity for morphology or life-history traits. Flat reaction norms, high among-clone variation, and low coefficients of variation (relative to the sexual population) are in accordance with the FPV model for the origin of clonal lineages. We also measured the prevalence of infection by trematode larvae to determine whether clones are inherently more or less infectable, or whether they are freezing phenotypic variation for resistance from the sexual population. We did this in the deep habitats of the lake where recycling of the parasite by the vertebrate host is unlikely, thereby reducing the complications raised by frequency-dependent responses of parasites to host genotypes. We found no indication that clones are either more or less infectable than the resident sexual population. Taken together, our results suggest that phenotypic variation for both life-history traits and resistance to parasites is frozen by clones from the local sexual population.     

Incidence of “Candidatus Liberibacter asiaticus” in a Florida population of Asian citrus psyllid

The incidence of a bacterium “Candidatus Liberibacter asiaticus” was assessed in a Florida population of Asian citrus psyllid, Diaphorina citri. The bacterium is the presumed causal agent of Asiatic huanglongbing, a serious citrus disease. Adult D. citri were periodically collected between May 2010 and September 2012 in a block of diseased trees located in east‐central Florida. The psyllids were individually subjected to molecular analyses (quantitative polymerase chain reaction assays using HLBaspr primers) to determine whether the bacterium was present and, if so, the population level of the pathogen based on qPCR cycle threshold (CT) values. Significantly greater percentages of females tested positive for the pathogen than males, but there were no significant differences between females and males with respect to population levels of the pathogen within the psyllids. No significant differences were found among the three D. citri colour morphs with respect to percentages of adults testing positive for the pathogen. Among 47 sample dates, a mean of 17.5% of adults per sample date tested positive (CT < 36) for the pathogen with a mean CT value of 31.1. The incidence of the pathogen was generally higher during late fall or early winter and often lower during mid‐ to late summer. There was a significant negative correlation between percentages of D. citri testing positive and air temperature. Increases in the incidence of the pathogen may not necessarily correspond to increases in transmission, as a number of factors both internal and external to D. citri can influence transmission. Transmission rates may be highest during periods when D. citri infestation levels are large, a high percentage of adults carry a high population of the pathogen in their salivary glands, and citrus flush is abundant.     

Individual acquisition of “stick pounding” behavior by naïve chimpanzees

Many studies investigating culture in nonhuman animals tend to focus on the inferred need of social learning mechanisms that transmit the form of a behavior to explain the population differences observed in wild animal behavioral repertoires. This research focus often results in studies overlooking the possibility of individuals being able to develop behavioral forms without requiring social learning. The disregard of individual learning abilities is most clearly observed in the nonhuman great ape literature, where there is a persistent claim that chimpanzee behaviors, in particular, require various forms of social learning mechanisms. These special social learning abilities have been argued to explain the acquisition of the relatively large behavioral repertoires observed across chimpanzee populations. However, current evidence suggests that although low‐fidelity social learning plays a role in harmonizing and stabilizing the frequency of behaviors within chimpanzee populations, some (if not all) of the forms that chimpanzee behaviors take may develop independently of social learning. If so, they would be latent solutions—behavioral forms that can (re‐)emerge even in the absence of observational opportunities, via individual (re)innovations. Through a combination of individual and low‐fidelity social learning, the population‐wide patterns of behaviors observed in great ape species are then established and stably maintained. This is the Zone of Latent Solutions (ZLS) hypothesis. The current study experimentally tested the ZLS hypothesis for pestle pounding, a wild chimpanzee behavior. We tested the reinnovation of this behavior in semi‐wild chimpanzees at Chimfunshi Wildlife Orphanage in Zambia, Africa, (N = 90, tested in four social groups). Crucially, all subjects were naïve to stick pounding before testing. Three out of the four tested groups reinnovated stick pounding—clearly demonstrating that this behavioral form does not require social learning. These findings provide support for the ZLS hypothesis alongside further evidence for the individual learning abilities of chimpanzees.     

Strong “bottom‐up” influences on small mammal populations: State‐space model analyses from long‐term studies

“Bottom‐up” influences, that is, masting, plus population density and climate, commonly influence woodland rodent demography. However, “top‐down” influences (predation) also intervene. Here, we assess the impacts of masting, climate, and density on rodent populations placed in the context of what is known about “top‐down” influences. To explain between‐year variations in bank vole Myodes glareolus and wood mouse Apodemus sylvaticus population demography, we applied a state‐space model to 33 years of catch‐mark‐release live‐trapping, winter temperature, and precise mast‐collection data. Experimental mast additions aided interpretation. Rodent numbers in European ash Fraxinus excelsior woodland were estimated (May/June, November/December). December–March mean minimum daily temperature represented winter severity. Total marked adult mice/voles (and juveniles in May/June) provided density indices validated against a model‐generated population estimate; this allowed estimation of the structure of a time‐series model and the demographic impacts of the climatic/biological variables. During two winters of insignificant fruit‐fall, 6.79 g/m² sterilized ash seed (as fruit) was distributed over an equivalent woodland similarly live‐trapped. September–March fruit‐fall strongly increased bank vole spring reproductive rate and winter and summer population growth rates; colder winters weakly reduced winter population growth. September–March fruit‐fall and warmer winters marginally increased wood mouse spring reproductive rate and September–December fruit‐fall weakly elevated summer population growth. Density dependence significantly reduced both species' population growth. Fruit‐fall impacts on demography still appeared after a year. Experimental ash fruit addition confirmed its positive influence on bank vole winter population growth with probable moderation by colder temperatures. The models show the strong impact of masting as a “bottom‐up” influence on rodent demography, emphasizing independent masting and weather influences; delayed effects of masting; and the importance of density dependence and its interaction with masting. We conclude that these rodents show strong “bottom‐up” and density‐dependent influences on demography moderated by winter temperature. “Top‐down” influences appear weak and need further investigation.     

Evaluating the “recovery level” of endangered species without prior information before alien invasion

For maintaining social and financial support for eradication programs of invasive species, quantitative assessment of recovery of native species or ecosystems is important because it provides a measurable parameter of success. However, setting a concrete goal for recovery is often difficult owing to lack of information prior to the introduction of invaders. Here, we present a novel approach to evaluate the achievement level of invasive predator management based on the carrying capacity of endangered species estimated using long‐term monitoring data. In Amami‐Oshima Island, Japan, where the eradication project of introduced small Indian mongoose is ongoing since 2000, we surveyed the population densities of four endangered species threatened by the mongoose (Amami rabbit, the Otton frog, Amami tip‐nosed frog, and Amami Ishikawa's frog) at four time points ranging from 2003 to 2011. We estimated the carrying capacities of these species using the logistic growth model combined with the effects of mongoose predation and environmental heterogeneity. All species showed clear tendencies toward increasing their density in line with decreased mongoose density, and they exhibited density‐dependent population growth. The estimated carrying capacities of three endangered species had small confidence intervals enough to measure recovery levels by the mongoose management. The population density of each endangered species has recovered to the level of the carrying capacity at about 20–40% of all sites, whereas no individuals were observed at more than 25% of all sites. We propose that the present approach involving appropriate monitoring data of native organism populations will be widely applicable to various eradication projects and provide unambiguous goals for management of invasive species.     

“Stepping-sticks” and “seat-sticks”: New types of tools used by wild chimpanzees (Pan troglodytes) in Sierra Leone

In Tenkere, Sierra Leone, a community of wild chimpanzees (Pan troglodytes verus) spent long hours eating the fruits and flowers of the Kapok (Ceiba pentandra) tree. The branches of this species are covered in sharp thorns which make movement in their high canopies problematic for the chimpanzees. In an apparent attempt to increase their mobility and to ease the discomfort of lengthy bouts of eating in these trees, some of the Tenkere chimpanzees have been observed using stick tools as foot (“stepping-sticks”) and body (“seat-sticks”) protection against the painful thorns. This form of tool-using is culturally unique to the Tenkere chimpanzees, as at other sites where these apes have been observed eating parts of kapok trees, there are no published records of this tool technology. In three of the stepping-stick tool use incidents, the chimpanzee used the tool(s), held between their greater and lesser toes, in locomotion. This form of tool use is the first recorded case of habitually used tools that can be justifiably categorized as being “worn” by any known wild population of Pan troglodytes. Am J Primatol 41:45–52, 1997. © 1997 Wiley-Liss, Inc.     

Genetic diversity of small populations: Not always “doom and gloom”?

Is a key theory of evolutionary and conservation biology—that loss of genetic diversity can be predicted from population size—on shaky ground? In the face of increasing human‐induced species depletion and habitat fragmentation, this question and the study of genetic diversity in small populations are paramount to understanding the limits of species’ responses to environmental change and to providing remedies to endangered species conservation. Few empirical studies have investigated to what degree some small populations might be buffered against losses of genetic diversity. Even fewer studies have experimentally tested the potential underlying mechanisms. The study of Schou, Loeschcke, Bechsgaard, Schlotterer, and Kristensen ( 2017 ) in this issue of Molecular Ecology is elegant in combining classic common garden experimentation with population genomics on an iconic experimental model species (Drosophila melanogaster). The authors reveal a slower rate of loss of genetic diversity in small populations under varying thermal regimes than theoretically expected and hence an unexpected retention of genetic diversity. They are further able to hone in on a plausible mechanism: associative overdominance, wherein homozygosity of deleterious recessive alleles is especially disfavoured in genomic regions of low recombination. These results contribute to a budding literature on the varying mechanisms underlying genetic diversity in small populations and encourage further such research towards the effective management and conservation of fragmented or endangered populations.     

Intraspecific variability in the “vowel”‐like sounds of beluga whales (Delphinapterus leucas): Intra‐ and interpopulation comparisons

The beluga whale (Delphinapterus leucas) has a rich and complicated vocal repertoire. However, different populations use similar and common types of signals. We studied physical features of one of these types, “vowels,” in three Russian populations: the White Sea population (European North), the Chukotka population (the Bering Sea, Chukotka), and the Okhotsk Sea population (Russian Far East) as well as in four summer aggregations of the White Sea belugas over several years in duration. The pulse repetition rate (PRR) at half of the duration of the signal was measured. We found that the PRR of “vowels” collected in the same summer aggregation during different years is stable in time but varies between locations. The degree of variation corresponds with the geographic distance between different locations. Significant differences were discovered between populations separated by thousands of kilometers, and to a lesser extent, between summer aggregations inhabiting different bays of the White Sea. The variation in PRR between the locations can be caused by the divergence of signals owing to the accumulation of random errors during transmission of these signals from generation to generation, which progressed independently in different summer aggregations and populations.     

Genomic insight into “sky island” species diversification in a mountainous biodiversity hotspot

“Sky island” species diversification contributes greatly to mountainous biodiversity. However, the underlying genomic divergence and the inferred drivers remain largely unknown. In this study, we examined the diversification history of five diploid species with three exclusively endemic to the sky islands (mountains) of the Himalaya–Hengduan Mountains biodiversity hotspot. All of them together comprise a clade of the genus Eutrema (Brassicaceae). We resequenced genomes of multiple individuals of the found populations for each species. We recovered the inconsistent phylogenetic relationships between plastome and nuclear‐genome trees for one species. Based on nuclear population genomic data, we detected high genetic divergence between five species with limited gene flow. Four species seemed to diverge mainly through geographical isolation, whereas one arose through hybrid origin. The origins of the sampled five species were dated to within the late Miocene when mountains were uplifted and climates oscillated. All species decreased their population sizes since the inferred origin of each species initially, but only two of them expanded after the Last Glacial Maximum. Together, these findings suggest that geographic isolation plays an important role in driving the sky island species diversification of the sampled species in addition to the occasional gene flow that might have led to the hybrid origin of some sky island species, similar to the species diversification of sea islands.     

THE “BIOTYPES” OF THE RICE BROWN PLANTHOPPER,NILAPARVATA LUGENS

From previous studies, the biological nature of the so-called biotypes of N. lugens is obscure. Experiments on biotypes 1, 2 and 3 from the Philippines demonstrated that they lacked significant breeding barriers. Inbred biotype cultures showed considerable variation and overlap between each other in virulence. A field population from the Philippines was similarly variable and included individuals which could be attributed to different biotypes. It is concluded that the use of the term biotype in this species is biologically misleading and undesirable.

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Résumé La nature biologique de ce qui a été appelé des biotypes de Nilaparvata lugens, paraît obscure si l'on se réfère aux études antérieures. Des expériences sur les biotypes 1, 2 et 3 des Philippines révèlent qu'ils ne présentent pas de barrières sexuelles significatives. Les élevages consanguins de biotypes présentent une variabilité considérable, et les virulances des biotypes se chevauchent les unes les autres. De même une population récoltée dans les çhamps aux Philippines était hétérogène et comprenait des individus qui auraient pu être rattachés à différents biotypes. On peut en conclure que le terme de biotype est, pour cette espèce, inapproprié et indésirable.

     

Transcriptome analysis reveals the difference between “healthy” and “common” aging and their connection with age‐related diseases

A key goal of aging research was to understand mechanisms underlying healthy aging and develop methods to promote the human healthspan. One approach is to identify gene regulations unique to healthy aging compared with aging in the general population (i.e., “common” aging). Here, we leveraged Genotype‐Tissue Expression (GTEx) project data to investigate “healthy” and “common” aging gene expression regulations at a tissue level in humans and their interconnection with diseases. Using GTEx donors' disease annotations, we defined a “healthy” aging cohort for each tissue. We then compared the age‐associated genes derived from this cohort with age‐associated genes from the “common” aging cohort which included all GTEx donors; we also compared the “healthy” and “common” aging gene expressions with various disease‐associated gene expressions to elucidate the relationships among “healthy,” “common” aging and disease. Our analyses showed that 1. GTEx “healthy” and “common” aging shared a large number of gene regulations; 2. Despite the substantial commonality, “healthy” and “common” aging genes also showed distinct function enrichment, and “common” aging genes had a higher enrichment for disease genes; 3. Disease‐associated gene regulations were overall different from aging gene regulations. However, for genes regulated by both, their regulation directions were largely consistent, implying some aging processes could increase the susceptibility to disease development; and 4. Possible protective mechanisms were associated with some “healthy” aging gene regulations. In summary, our work highlights several unique features of GTEx “healthy” aging program. This new knowledge could potentially be used to develop interventions to promote the human healthspan.     

Comparisons of population density and genetic diversity in artificial and wild populations of an arborescent coral,Acropora yongei: implications for the efficacy of “artificial spawning hotspots”

We are developing techniques to restore coral populations by enhancing larval supply using “artificial spawning hotspots” that aggregate conspecific adult corals. However, no data were available regarding how natural larval supply from wild coral populations is influenced by fertilization rate and how this is in turn affected by local population density and genetic diversity. Therefore, we assessed population density and genetic diversity of a wild, arborescent coral, Acropora yongei, and compared these parameters with those of an artificially established A. yongei population in the field. The population density of wild arborescent corals was only 0.27% of that in the artificial population, even in a high‐coverage area. Genetic diversity was also low in the wild population compared with the artificial population, and approximately 10% of all wild colonies were clones. Based on these results, the larval supply in the artificial population was estimated to be at least 1,400 times higher than that in wild A. yongei populations for the same area of adult population.     

SELECTION AND THE “SEX-RATIO” POLYMORPHISM IN NATURAL POPULATIONS OF DROSOPHILA PSEUDOOBSCURA

“Sex-ratio” (SR) is a naturally occurring X-linked meiotic drive system, where the SR-X chromosome is transmitted to nearly all progeny of SR males. It occurs at frequencies of up to 25% in some populations of Drosophila pseudoobscura. Because of the twofold drive advantage, SR should rapidly fix in populations, causing the extinction of the species, unless opposed by strong selection. I examine several of the adult components of fitness, including the frequencies of all genotypic mating combinations, fertilities, and fecundities of flies from two populations in southeastern Arizona. Significant reduction of fecundity of SR/SR females was observed in the Tucson population. No evidence was found for either lower fertility or reduced mating success of SR males, relative to standard males. Most selection opposing SR appears to be operating at the larval stages in nature.     

Archeology and the dispersal of modern humans in Europe: Deconstructing the “Aurignacian”

Few would now dispute the reality of a major dispersal of anatomically and genetically modern human populations across Europe and western Asia centered broadly within the period from ca. 45,000 to 35,000 BP in terms of conventional radiocarbon dating, or between ca. 47,000 and 41,000 BP in terms of the most recent calibration of the radiocarbon timescale. 1 This can be supported equally from the direct skeletal evidence recovered from European and Near Eastern sites and from the closely similar conclusions drawn from studies of both the mitochondrial and Y‐chromosome DNA evidence in modern European populations. 2 - 4 How far these new anatomically and genetically modern populations may or may not have interbred with the preceding Neanderthal populations in the different regions of Europe remains a matter of lively debate. 2 , 5 , 6 But the reality of this modern human population dispersal itself is now almost universally accepted.