Drop In Population Size Research Articles

Advancing equine genomics: the development of a high density Axiom_Ashwa SNP chip for Indian horses and ponies.

The unique horse and pony breeds of India are declining at an alarming rate. These horses have been integral to the Indian culture and customs for centuries and represent a valuable genetic resource. It is imperative to harness the potential of this equine genetic resource that urgently needs conservation. The study highlights the design and development of a high density SNP array, the Axiom_Ashwa to aid in the genetic analysis and conservation efforts for Indian horse and pony breeds. With 613,950 SNPs, this chip offers extensive genome coverage having an average inter-marker distance of 4kb. The Axiom_Ashwa has been validated on a larger set of diverse indigenous samples as well as Thoroughbreds, demonstrating a high call rate of 99.4% and robustness for genotyping indigenous breeds. Linkage disequilibrium (LD) analysis showed higher average LD in Indian breeds compared to exotic breeds, suggesting a limited effective population size and recent bottlenecks. Phylogenetic and population stratification analyses using PCA and DAPC clearly distinguished horses, ponies and Thoroughbreds, confirming the efficacy of the Axiom_Ashwa chip. These findings underscore the urgent need for conservation efforts for Indian horse breeds, which have experienced significant drop in population size. The Axiom_Ashwa SNP chip offers advantages such as cost-effectiveness and high throughput, providing a more accurate genetic representation of Indian horses.

Automated face recognition using deep neural networks produces robust primate social networks and sociality measures

AbstractLongitudinal video archives of behaviour are crucial for examining how sociality shifts over the lifespan in wild animals. New approaches adopting computer vision technology hold serious potential to capture interactions and associations between individuals in video at large scale; however, such approaches need a priori validation, as methods of sampling and defining edges for social networks can substantially impact results.Here, we apply a deep learning face recognition model to generate association networks of wild chimpanzees using 17 years of a video archive from Bossou, Guinea. Using 7 million detections from 100 h of video footage, we examined how varying the size of fixed temporal windows (i.e. aggregation rates) for defining edges impact individual‐level gregariousness scores.The highest and lowest aggregation rates produced divergent values, indicating that different rates of aggregation capture different association patterns. To avoid any potential bias from false positives and negatives from automated detection, an intermediate aggregation rate should be used to reduce error across multiple variables. Individual‐level network‐derived traits were highly repeatable, indicating strong inter‐individual variation in association patterns across years and highlighting the reliability of the method to capture consistent individual‐level patterns of sociality over time. We found no reliable effects of age and sex on social behaviour and despite a significant drop in population size over the study period, individual estimates of gregariousness remained stable over time.We believe that our automated framework will be of broad utility to ethology and conservation, enabling the investigation of animal social behaviour from video footage at large scale, low cost and high reproducibility. We explore the implications of our findings for understanding variation in sociality patterns in wild ape populations. Furthermore, we examine the trade‐offs involved in using face recognition technology to generate social networks and sociality measures. Finally, we outline the steps for the broader deployment of this technology for analysis of large‐scale datasets in ecology and evolution.

Rapid polygenic response to secondary contact in a hybrid species.

Secondary contact between closely related species can have genetic consequences. Competition for essential resources may lead to divergence in heritable traits that reduces interspecific competition leading to increased rate of genetic divergence. Conversely, hybridization and backcrossing can lead to genetic convergence. Here, we study a population of a hybrid species, the Italian sparrow (Passer italiae), before and after it came into secondary contact with one of its parent species, the Spanish sparrow (P. hispaniolensis), in 2013. We demonstrate strong consequences of interspecific competition: Italian sparrows were kept away from a popular feeding site by its parent species, resulting in poorer body condition and a significant drop in population size. Although no significant morphological change could be detected, after only 3 years of sympatry, the Italian sparrows had diverged significantly from the Spanish sparrows across a set of 81 protein-coding genes. These temporal genetic changes are mirrored by genetic divergence observed in older sympatric Italian sparrow populations within the same area of contact. Compared with microallopatric birds, sympatric ones are genetically more diverged from Spanish sparrows. Six significant outlier genes in the temporal and spatial comparison (i.e. showing the greatest displacement) have all been found to be associated with learning and neural development in other bird species.

Status of the Northern Silvery Grebe Podiceps juninensis in the northern Andes: recent changes in distribution, population trends and conservation needs

SummaryThe Northern Silvery Grebe Podiceps juninensis is an aquatic bird species considered Vulnerable to extinction in Ecuador and Endangered in Colombia. Globally the species is considered Near Threatened. Herein we report recent changes in distribution and population trends for the subpopulation in the northern Andes (Ecuador, Colombia), which is small and isolated. The Northern Silvery Grebe has undergone two documented extirpations, and at least one colonisation event, over the last three decades. More than 90% of the subpopulation relies on two wetlands, La Mica and Colta lakes in Ecuador, with the latter facing an accelerated sedimentation process which jeopardizes the fate of the wetland, and the species, in the mid-term. The population of La Mica lost 80% of its birds in 2000 after the damming of the lake, but then remained stable over our census period (2004–2013). In contrast, the Colta population results from a recent colonisation in the early 2000s, and has experienced an exponential growth since then (annual population multiplication rate: 1.464). The growth of this population is so fast that it must include an important contribution of immigrants. The temporal coincidence between the drop in population size at lake La Mica and the colonisation of lake Colta suggests that the Colta population was founded by immigrants from La Mica. Finally, the absence of current reports of the species at wetlands in Colombia suggests that the species remains at very low numbers, bolstering the shrinkage in northern distribution.

HELGA: a heterogeneous encoding lifelike genetic algorithm for population evolution modeling and simulation

Today, there is a substantial need for population evolution modeling in multidisciplinary research areas, such as social sciences (sociology, anthropology etc.), which can neither be solved formally, nor empirically at global scale, thus requiring the development of heuristic techniques, like evolutionary algorithms. Therefore, existent methodologies of social simulation can be extended from microenvironments to large scale modeling of extremely complex systems, as it is the case of human evolution. The modeling of population evolution prediction is currently used in high interest areas, from migration flows, to financial crisis simulation, to the free-market economy models, as well as multi-national family dynamics and cultural aspects. The high performance of evolutionary computing has been already proven in the context of virus population evolution, be they biological or cybernetic, thus making them the perfect method for our endeavour. This paper presents the design and implementation of a soft computing application, namely HELGA--heterogeneous encoding lifelike genetic algorithm. HELGA was designed for the modeling and simulation of Earth population evolution, on a global scale, throughout multiple historical eras. The model shows the tendency of human evolution towards one mixed race. The algorithm takes into account the influence of social factors, such as the Industrial Revolution or the discovery of the New World. Our method, for which all constraints have been based on validated research, has aligned precisely to real historical events: it anticipated the end of antiquity, the industrial era, the baby boom phenomenon and so on. For example, the poor health conditions of the Middle Ages have caused a drastic drop in population size. The presented model shows the valiant result of one final race, and although this theory cannot be formally proved in the present, we consider that our results can be used as hypothesis for future social science research. Also, HELGA can be extended with new capabilities and constraints.

Genetic analysis of the Venezuelan Criollo horse

Various horse populations in the Americas have an origin in Spain; they are remnants of the first livestock introduced to the continent early in the colonial period (16th and 17th centuries). We evaluated genetic variability within the Venezuelan Criollo horse and its relationship with other horse breeds. We observed high levels of genetic diversity within the Criollo breed. Significant population differentiation was observed between all South American breeds. The Venezuelan Criollo horse showed high levels of genetic diversity, and from a conservation standpoint, there is no immediate danger of losing variation unless there is a large drop in population size.

Modelling crayfish population dynamics using catch data: A size-structured model

In this study we explore a rather unique time series (1979–2002) of catch data of the crayfish Astacus astacus in Lake Steinsfjorden (SE Norway) in combination with temperature data and data on Canadian pondweed Elodea canadensis coverage. In 1977, E. canadensis was for the first time observed in the lake. Over the following years, the plant established dense covers over large parts of the shallow areas, excluding the crayfish from these areas and causing a sudden drop in population size. A size-structured model with bi-stability including a range of observed stage-specific life-cycle attributes (e.g. growth, fecundity, fertility, sex-ratio), population specific parameters and density-dependant (shelters, cannibalism, unspecified predators, competition between individuals, catch, number of traps) as well as density independent factors (temperature and Elodea coverage) were constructed to evaluate the various drivers for the population dynamics, and as a predictive tool for assessing the effects of future changes. Our model revealed that the decline primarily was due to density-dependant effect of the Elodea expansion with reduced number of hides and thus increased risk for predation and cannibalism, but also that temperature played an important role related to recruitment. The model should be relevant for crayfish stock management in general, and by demonstrating the major role of temperature, it is also relevant for predicting population responses under a changing climate. The model should also be applicable to other crustaceans and species with discrete growth and late maturation.

The role of density-dependent individual growth in the persistence of freshwater salmonid populations

Theoretical and empirical models of populations dynamics have paid little attention to the implications of density-dependent individual growth on the persistence and regulation of small freshwater salmonid populations. We have therefore designed a study aimed at testing our hypothesis that density-dependent individual growth is a process that enhances population recovery and reduces extinction risk in salmonid populations in a variable environment subject to disturbance events. This hypothesis was tested in two newly introduced marble trout (Salmo marmoratus) populations living in Slovenian streams (Zakojska and Gorska) subject to severe autumn floods. We developed a discrete-time stochastic individual-based model of population dynamics for each population with demographic parameters and compensatory responses tightly calibrated on data from individually tagged marble trout. The occurrence of severe flood events causing population collapses was explicitly accounted for in the model. We used the model in a population viability analysis setting to estimate the quasi-extinction risk and demographic indexes of the two marble trout populations when individual growth was density-dependent. We ran a set of simulations in which the effect of floods on population abundance was explicitly accounted for and another set of simulations in which flood events were not included in the model. These simulation results were compared with those of scenarios in which individual growth was modelled with density-independent Von Bertalanffy growth curves. Our results show how density-dependent individual growth may confer remarkable resilience to marble trout populations in case of major flood events. The resilience to flood events shown by the simulation results can be explained by the increase in size-dependent fecundity as a consequence of the drop in population size after a severe flood, which allows the population to quickly recover to the pre-event conditions. Our results suggest that density-dependent individual growth plays a potentially powerful role in the persistence of freshwater salmonids living in streams subject to recurrent yet unpredictable flood events.

Past and present distribution of badgers Meles meles in the Copenhagen area

Two surveys of badgers Meles meles in the Copenhagen area, one in 1973–1975 and one in 1983–1985, are presented. The data suggest a 33% decrease in the number of badgers in that 10-year period. Possible reasons for this drop in population size are discussed. Human disturbance seems to play a major role and depletion of habitat only a minor role. The Danish game bag records demonstrate a halving of the number of badgers shot during the last 30 years. Among other things, this probably reflects some decline of the badger population also outside the metropolitan area. It is suggested that the causes for the decline observed within the Copenhagen area might well be contributing to a decline in badgers in the rest of the country.

Population Dynamics of the Strawberry Aphid 1 in Southwestern Washington 2

Chaetosiphon fragaefolii (Cockerell) was studied to determine the factors regulating its populations. Fertilizers, irrigation, defoliation to stimulate production of new leaves, and removal of blossoms had only temporary effects or none on populations. Aphid populations were much larger on plants covered by cages in the field, indicating that predators were an important controlling factor. However, parasitized aphids were never found. Populations became even larger in an unheated greenhouse and remained large through the winter, even at subfreezing temperatures, whereas populations became low in field cages. Wind and rain probably are detrimental to the aphids. The field population always declined in the late summer, even in cages. Analysis of strawberry foliage showed that populations of this aphid tend to correlate with the concentration of nonreducing sugars (probably mostly sucrose). Decline in nutritional value of the leaves coupled with increasing predator populations are probably the prime reasons for the rapid drop in population size in mid- to late summer each year.