Approximately 50 ka, one or more subgroups of modern humans expanded from Africa to populate the rest of the world. Significant behavioral change accompanied this expansion, and archaeologists ...commonly seek its roots in the African Middle Stone Age (MSA; ∼200 to ∼50 ka). Easily recognizable art objects and “jewelry” become common only in sites that postdate the MSA in Africa and Eurasia, but some MSA sites contain possible precursors, especially including abstractly incised fragments of ocher and perforated shells interpreted as beads. These proposed art objects have convinced most specialists that MSA people were behaviorally (cognitively) modern, and many argue that population growth explains the appearance of art in the MSA and its post-MSA florescence. The average size of rocky intertidal gastropod species in MSA and later coastal middens allows a test of this idea, because smaller size implies more intense collection, and more intense collection is most readily attributed to growth in the number of human collectors. Here we demonstrate that economically important Cape turban shells and limpets from MSA layers along the south and west coasts of South Africa are consistently and significantly larger than turban shells and limpets in succeeding Later Stone Age (LSA) layers that formed under equivalent environmental conditions. We conclude that whatever cognitive capacity precocious MSA artifacts imply, it was not associated with human population growth. MSA populations remained consistently small by LSA standards, and a substantial increase in population size is obvious only near the MSA/LSA transition, when it is dramatically reflected in the Out-of-Africa expansion.
Respondent-driven sampling (RDS) employs a variant of a linktracing network sampling strategy to collect data from hard-toreach populations. By tracing the links in the underlying social network, the ...process exploits the social structure to expand the sample and reduce its dependence on the initial (convenience) sample. The current estimators of population averages make strong assumptions in order to treat the data as a probability sample. We evaluate three critical sensitivities of the estimators: (1) to bias induced by the initial sample, (2) to uncontrollable features of respondent behavior, and (3) to the without-replacement structure of sampling. Our analysis indicates: (1) that the convenience sample of seeds can induce bias, and the number of sample waves typically used in RDS is likely insufficient for the type of nodal mixing required to obtain the reputed asymptotic unbiasedness; (2) that preferential referral behavior by respondents leads to bias; (3) that when a substantial fraction of the target population is sampled the current estimators can have substantial bias. This paper sounds a cautionary note for the users of RDS. While current RDS methodology is powerful and clever, the favorable statistical properties claimed for the current estimates are shown to be heavily dependent on often unrealistic assumptions. We recommend ways to improve the methodology.
Sequential techniques can enhance the efficiency of the approximate Bayesian computation algorithm, as in Sisson et al.'s (2007) partial rejection control version. While this method is based upon the ...theoretical works of Del Moral et al. (2006), the application to approximate Bayesian computation results in a bias in the approximation to the posterior. An alternative version based on genuine importance sampling arguments bypasses this difficulty, in connection with the population Monte Carlo method of Cappé et al. (2004), and it includes an automatic scaling of the forward kernel. When applied to a population genetics example, it compares favourably with two other versions of the approximate algorithm.
We describe temporal changes in the genetic composition of a small anadromous Atlantic salmon (Salmo salar) population from South Newfoundland, an area where salmon populations are considered ...threatened (COSEWIC 2010). We examined the genetic variability (13 microsatellite loci) in 869 out‐migrating smolt and post‐spawning kelt samples, collected from 1985 to 2011 for a total of 22 annual collections and a 30 year span of assigned cohorts. We estimated the annual effective number of breeders (Nb) and the generational effective population size (Nₑ) through genetic methods and demographically using the adult sex ratio. Comparisons between genetic and demographic estimates show that the adult spawners inadequately explain the observed Nₑ estimates, suggesting that mature male parr are significantly increasing Nb and Nₑ over the study period. Spawning as parr appears to be a viable and important strategy in the near absence of adult males.
Noninvasive genetic methods can be used to estimate animal abundances and offer several advantages over conventional methods. Few attempts have been made, however, to evaluate the accuracy and ...precision of the estimates. We compared four methods of estimating population size based on fecal sampling. Two methods used rarefaction indices and two were based on capture-mark-recapture (CMR) estimators, one combining genetic and field data. Volunteer hunters and others collected 1904 fecal samples over 2 consecutive years in a large area containing a well-studied population of brown bears (Ursus arctos). On our$49, \!000\!\!-\!\!km^2$study area in south-central Sweden, population size estimates ranged from 378 to 572 bears in 2001 and 273 to 433 bears in 2002, depending on the method of estimation used. The estimates from the best model in the program MARK appeared to be the most accurate, based on the minimum population size estimate from radio-marked bears in a subsection of our sampling area. In addition, MARK models included heterogeneity and temporal variation in detection probabilities, which appeared to be present in our samples. All methods, though, incorrectly suggested a biased sex ratio, probably because of sex differences in detection probabilities and low overall detection probabilities. The population size of elusive animals can be estimated reliably over large areas with noninvasive genetic methods, but we stress the importance of an adequate and well-distributed sampling effort. In cases of biased sampling, calibration with independent estimates may be necessary. We recommend that this noninvasive genetic approach, using the MARK models, be used in the future in areas where sufficient numbers of volunteers can be mobilized.
Many species that are birthed in one location and become reproductive in another location can be treated as if in a one-dimensional habitat where dispersal is biased downstream. One example of such ...is planktonic larvae that disperse in coastal oceans, rivers, and streams. In these habitats, the dynamics of the dispersal are dominated by the movement of offspring in one direction and the distance between parents and offspring in the other direction does not matter. We study an idealized species with non-overlapping generations in a finite linear habitat that has no larval input from outside of the habitat and is therefore isolated from other populations. The most non-realistic assumption that we make is that there are non-overlapping generations, and this is an assumption to be considered in future work. We find that a biased dispersal in the habitat reduces the average time to the most recent common ancestor and causes the average location of the most recent common ancestor to move from the center of the habitat to the upstream edge of the habitat. Due to the decrease in the time to the most recent common ancestor and the shift of the average location to the upstream edge, the effective population size (Ne) no longer depends on the census size and is dependent on the dispersal statistics. We determine the average time and location of the most recent common ancestor as a function of the larval dispersal statistics. The location of the most recent common ancestor becomes independent of the length of the habitat and is only dependent on the location of the upstream edge and the larval dispersal statistics.
Using archaeological data, this paper investigates past population trends in Ireland as a response to recent genomic studies that have identified admixture signals in the genomes of Irish people ...caused by historically-recorded migration events. Among these was Norse settlement in the 9th-10th Centuries CE, which has a greater than expected signal in the contemporary population of the island. Here, we contextualise these discoveries using a large database of recently discovered archaeological sites with radiocarbon dates that we have analysed using Kernel Density Estimation techniques. We argue that the Viking migrations occurred following a 300-year period of population decrease in Ireland. This new, data-driven synthesis of the archaeological record contrasts with previous accounts of early medieval Ireland as a period of ever-growing expansion and progression. However, this new interpretation is also aligned to evidence for economic and environmental change, including recent discoveries concerning the soil nitrogen cycle and agricultural intensification. We compare historical evidence for Viking migrations to later episodes of migration between Britain and Ireland, where more details are known about the size of the incoming groups, ultimately wishing to confront the opinion that past population sizes cannot be fathomed for cultures without documentary records. Through comparison with historic analyses and census records, we make broad estimates of absolute population size in Ireland since prehistoric times, including during these demographic events, and argue that much value is added to genomic evidence for migration when these points in time are contextualised in terms of evolving population trends.
•A database containing over 8000 radiocarbon dates of human activity in Ireland has been assembled.•Contextualizing the data for the period 400 to 1200 CE reveals a pronounced oscillation in activity throughout the landscape.•A long-term population model has been developed for Ireland using these radiocarbon data and historical records.•We suggest haplotype admixture in Ireland took place in the context of long term population decline.•These results mirror recent palaeoisotope studies of intensification.
Abstract
The effective size of a population (Ne) in the recent past can be estimated through analysis of identity-by-descent (IBD) segments. Several methods have been developed for estimating Ne from ...autosomal IBD segments, but no such effort has been made with X chromosome IBD segments. In this work, we propose a method to estimate the X chromosome effective population size from X chromosome IBD segments. We show how to use the estimated autosome Ne and X chromosome Ne to estimate the female and male effective population sizes. We demonstrate the accuracy of our autosome and X chromosome Ne estimation with simulated data. We find that the estimated female and male effective population sizes generally reflect the simulated sex-specific effective population sizes across the past 100 generations but that short-term differences between the estimated sex-specific Ne across tens of generations may not reliably indicate true sex-specific differences. We analyzed the effective size of populations represented by samples of sequenced UK White British and UK Indian individuals from the UK Biobank.
Effective population size (Ne) in the recent past can be estimated through analysis of identity-by-descent (IBD) segments. In this work, Cai et al. propose a method to estimate the X chromosome effective population size from X chromosome IBD segments. The authors show how to use the estimated autosome Ne and X chromosome Ne to estimate female and male effective population sizes.
•Differential Evolution algorithms applied to ANN training suffer from stagnation.•The lack of difference vectors of small magnitude is noted during ANN training by Differential Evolution methods.•In ...case of benchmark problems the lack of difference vectors of small magnitude is only occasionally observed.•DEGL algorithm outperforms other Differential Evolution variants for ANN training.•Best algorithms found for benchmark problems do not perform well for ANN training.
Large number of population-based Differential Evolution algorithms has been proposed in the literature. Their good performance is often reported for benchmark problems. However, when applied to Neural Networks training for regression, these methods usually perform poorer than classical Levenberg–Marquardt algorithm. The major aim of the present paper is to clarify, why? In this research, in which Neural Networks are used for a real-world regression problem, it is empirically shown that various Differential Evolution algorithms are falling into stagnation during Neural Network training. It means that after some time the individuals stop improving, or improve very occasionally, although the population diversity remains high. Similar behavior of Differential Evolution algorithms is observed for some, but not the majority of, benchmark problems. In the paper the impact of Differential Evolution population size, the initialization range and bounds on Neural Networks performance is also discussed.
Among tested algorithms only the Differential Evolution with Global and Local neighborhood-based mutation operators performs better than the Levenberg–Marquardt algorithm for Neural Networks training. This version of Differential Evolution also shows the symptoms of stagnation, but much weaker than the other tested variants. To enhance exploitation in the final stage of Neural Networks training, it is proposed to merge the Differential Evolution with Global and Local neighborhood-based mutation operators algorithm with the Trigonometric mutation operator. This method does not rule out the stagnation problem, but slightly improves the performance of trained Neural Networks.
Effective, evidence‐based management is required to ensure long‐term coexistence between people and wildlife in an increasingly humanized world. Although behavioural individuality is recognized as a ...key factor affecting evolutionary and ecological processes, it has rarely been explicitly assessed in relation to human–wildlife conflicts. The ‘problem individual’ paradigm states that some conspecifics within a given population have a disproportionately large contribution to conflicts. To the best of our knowledge, no studies have so far systematically tested this assumption in large carnivores.
Here, we investigated the variation in conflict behaviour among brown bears Ursus arctos within the population inhabiting the Polish Eastern Carpathians. We inspected all sites notified as damaged by bears in 2014–2017 to determine the number and sex of the individuals involved. We conducted systematic noninvasive genetic sampling to estimate the size of the local population by spatially explicit capture–recapture models. We assessed the fraction and sex ratio of damage‐making bears in relation to the population, as well as the behavioural patterns by classifying and differentiating between occasional and repetitive damage‐makers.
Approximately one‐third of the estimated 72 (95% CI 45.2–115.5) brown bears inhabiting the Polish Eastern Carpathians were responsible for damage occurrence in the region. The majority of damage‐makers were female (65% vs. 35% of male), which reflected the sex ratio of the local population (0.57). Thirty‐three per cent of the damage‐making bears (i.e. nine individuals) were classified as ‘problem individuals’, exhibiting repetitive conflict behaviour.
Synthesis and applications. This study provides evidence of intraspecific differences in conflict behaviour in a large carnivore species, the brown bear, and indicates that damage‐making behaviour is not exhibited with the same frequency by all individuals within a population. Managers and policy‐makers should be aware that targeting individuals involved in conflicts without reference to the whole population may lead to misleading conclusions or an incomplete picture of the mechanisms underlying the conflicts, and thus, to mismanagement. Unravelling the behavioural patterns of individual engagement in damage through large‐scale and population‐wide studies is needed to accurately assess the magnitude of damage and enhance human–wildlife coexistence in areas experiencing conflicts.
Abstrakt
Skuteczne, oparte na dowodach naukowych zarządzanie populacjami gatunków chronionych jest konieczne, aby zapewnić długoterminowe współistnienie ludzi i dzikich zwierząt w świecie coraz bardziej zdominowanym przez człowieka. Chociaż indywidualność zachowań jest uznawana za kluczowy czynnik wpływający na procesy ewolucyjne i ekologiczne, rzadko bywa oceniana w odniesieniu do konfliktów człowiek–dzikie zwierzęta. Paradygmat ‘osobników problemowych’ zakłada, iż niektóre osobniki w danej populacji mają nieproporcjonalnie duży udział w konfliktach. Według naszej wiedzy, założenie to nie było jak dotąd testowane w sposób systematyczny w populacji dużych drapieżników.
W niniejszej pracy zbadaliśmy międzyosobnicze zróżnicowanie zachowań konfliktowych niedźwiedzi brunatnych Ursus arctos w populacji zamieszkującej polską część Karpat Wschodnich. Dokonaliśmy inspekcji terenowych szkód zgłoszonych jako wyrządzone przez niedźwiedzie w latach 2014–2017, aby określić liczbę i płeć osobników zaangażowanych w konflikt. Ponadto, przeprowadziliśmy systematyczny i nieinwazyjny zbiór prób do badań genetycznych w celu oszacowania wielkości lokalnej populacji za pomocą przestrzennych modeli wielokrotnych złowień (spatially explicit capture–recapture). Oceniliśmy udział niedźwiedzi wyrządzających szkody w odniesieniu do całej populacji oraz proporcję płci w tej grupie, a także wzorce zachowań rozróżniając sprawców szkód na okazjonalnych i powtarzalnych.
Około jedna trzecia z oszacowanych 72 (95% CI 45.2–115.5) niedźwiedzi brunatnych zamieszkujących polskie Karpaty Wschodnie była odpowiedzialna za powodowanie szkód w regionie. Wśród sprawców szkód przeważały samice (65% vs. 35% samców), co odzwierciedlało proporcję płci w lokalnej populacji (0.57). Trzydzieści trzy procent niedźwiedzi wyrządzających szkody (tj. dziewięć osobników) zostało zakwalifikowanych jako osobniki problemowe, wykazujące powtarzalne zachowania konfliktowe.
Synteza i wnioski. Nasze badanie dostarcza dowodów na istnienie wewnątrzgatunkowych różnic w zachowaniach konfliktowych u dużego ssaka drapieżnego, niedźwiedzia brunatnego, i wskazuje, iż zachowania prowadzące do powstania szkód nie są przejawiane z taką samą częstością przez wszystkie osobniki w populacji. Zarządzający populacjami dzikich zwierząt powinni być świadomi, iż skupianie uwagi wyłącznie na osobnikach zaangażowanych w konflikt, bez odniesienia do całej populacji, może prowadzić do mylnych wniosków lub niepełnego obrazu mechanizmów leżących u podstaw konfliktu, a tym samym do niewłaściwego zarządzania. Odkrycie wzorców zachowań osobników zaangażowanych w szkody poprzez badania obejmujące całą populację jest konieczne, aby właściwie ocenić skalę szkód oraz polepszyć koegzystencję ludzi i zwierząt na obszarach, na których dochodzi do konfliktów.
This study provides evidence of intraspecific differences in conflict behaviour in a large carnivore species, the brown bear, and indicates that damage‐making behaviour is not exhibited with the same frequency by all individuals within a population. Managers and policy‐makers should be aware that targeting individuals involved in conflicts without reference to the whole population may lead to misleading conclusions or an incomplete picture of the mechanisms underlying the conflicts, and thus, to mismanagement. Unravelling the behavioural patterns of individual engagement in damage through large‐scale and population‐wide studies is needed to accurately assess the magnitude of damage and enhance human–wildlife coexistence in areas experiencing conflicts.
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