Small Local Populations Research Articles

Evolution of rarity and phylogeny determine above- and belowground biomass in plant-plant interactions.

Rare species are often considered inferior competitors due to occupancy of small ranges, specific habitats, and small local populations. However, the phylogenetic relatedness and rarity level (level 1-7 and common) of interacting species in plant-plant interactions are not often considered when predicting the response of rare plants in a biotic context. We used a common garden of 25 species of Tasmanian Eucalyptus, to differentiate non-additive patterns in the biomass of rare versus common species when grown in mixtures varying in phylogenetic relatedness and rarity. We demonstrate that rare species maintain progressively positive non-additive responses in biomass when interacting with phylogenetically intermediate, less rare and common species. This trend is not reflected in common species that out-performed in monocultures compared to mixtures. These results offer predictability as to how rare species' productivity will respond within various plant-plant interactions. However, species-specific interactions, such as those involving E. globulus, yielded a 97% increase in biomass compared to other species-specific interaction outcomes. These results are important because they suggest that plant rarity may also be shaped by biotic interactions, in addition to the known environmental and population factors normally used to describe rarity. Rare species may utilize potentially facilitative interactions with phylogenetically intermediate and common species to escape the effects of limiting similarity. Biotically mediated increases in rare plant biomass may have subsequent effects on the competitive ability and geographic occurrence of rare species, allowing rare species to persist at low abundance across plant communities. Through the consideration of species rarity and evolutionary history, we can more accurately predict plant-plant interaction dynamics to preserve unique ecosystem functions and fundamentally challenge what it means to be "rare".

A queueing system with an SIR-type infection

AbstractWe consider the propagation of a stochastic SIR-type epidemic in two connected populations: a relatively small local population of interest which is surrounded by a much larger external population. External infectives can temporarily enter the small population and contribute to the spread of the infection inside this population. The rules for entry of infectives into the small population as well as their length of stay are modeled by a general Markov queueing system. Our main objective is to determine the distribution of the total number of infections within both populations. To do this, the approach we propose consists of deriving a family of martingales for the joint epidemic processes and applying classical stopping time or convergence theorems. The study then focuses on several particular cases where the external infection is described by a linear branching process and the entry of external infectives obeys certain specific rules. Some of the results obtained are illustrated by numerical examples.

Moving towards local participation and comanagement of Tioman Island Marine Park

Tioman Archipelago is a Marine Protected Area (MPA) off the coast of Pahang, Malaysia. It is inhabited by a small local population that depends on tourism as its main source of income. Its rich biodiversity is the main attraction to visitors, yet it is threatened by the growing tourism market. In 1994 the waters extending 3.7 km from the shore surrounding the island were gazetted as an MPA under the provisions of the Fisheries Act of 1985. The Department of Fisheries Malaysia (DoF) is responsible for the management and enforcement of the MPA, with minimal or no involvement of the local communities. A study conducted by Reef Check Malaysia (RCM) in 2014 with the local communities revealed that the vast majority showed an interest in being involved in management and conservation efforts but did not have the qualifications or the means to do so. In 2015, the Tioman Marine Conservation Group (TMCG) was formalized as a platform for interested local communities to undergo a series of training programs to empower them in building ecological resilience and marine resource management processes. The TMCG has since executed many conservation programs including ghost net removals, mooring buoy management, coral predator control, coral rehabilitation, reef monitoring surveys, community consultations, promotion of responsible tourism standards, and cleanups. RCM provided training, oversight, and funding. As of 2023, there are 80 members from each of the island’s seven villages. In 2019 the TMCG was officially recognized by the DoF as one of its strategic partners under its Reef Care program. This paper details how Tioman Island Marine Park moves from a top-down management approach towards local participation and a comanagement approach.

Botrychium virginianum (Ophioglossaceae), a new species for the flora of Volyn Polissia (Ukraine)

During floristic surveys conducted in the southern part of Volyn Polissia (Rivne Region) in July 2021, a rare and relict species, Botrychium virginianum (Ophioglossaceae), was discovered for the first time in this area. According to the Ukrainian sozological data, the species is included in the category Endangered; using the IUCN categorization, it is considered as a Critically Endangered (CR) species of the flora of Ukraine. In Ukraine, where the southern border of the species range is located, 30 localities have been recorded until present, most of them prior to the first half of the 20th century. The reported location of B. virginianum is associated with the carbonate uplift of the first floodplain terrace of the right bank of the Horyn River within the boundaries of the Kostopil-Berezniv physiographic district of Volyn Polissia. A small local population consists of at least five individuals with high vitality. The ecological and phytocenotic conditions of the reported species habitat have been studied and its limiting factors have been clarified. It is recommended to include this site with a cluster of rare species of the flora in the Suskyi Botanical Reserve of national importance, which is located nearby.

The Brigands’ Song among the Ngạn People in Northern Vietnam

Abstract The Ngạn people are a small local population of Tai-language speakers now living in the eastern districts of Cao Bằng province in northern Vietnam. They are said to be descendants of mercenary soldiers hired by the Mạc royal court during the 17th century. It is the aim of this article to investigate where they came from, using Vietnamese and Chinese ethnological studies, on-site fieldwork and analysis of song texts, supplemented by information from a ritual text and a family register. My conclusion is that the original homeland of the Ngạn was in the Youjiang River valley in west-central Guangxi. Numerous strands of evidence point to a strong connection with the native chieftaincy of Tianzhou and the neighbouring chieftaincy of Si’en.

New records of Capreolus capreolus Linnaeus, 1758 in the Monti Lepini (Lazio, Central Italy)

The Roe Deer was present in the Monti Lepini (Southern Lazio) up to the first half of the nineteenth century, then it went locally extinct. In this note we report four new records of this species that testify for the current existence of a (likely very small) local population, which would represent the only other wild ungulate in the area, in addition to the very common Wild Boar.

Comparison of Soft Indicator and Poisson Kriging for the Noise-Filtering and Downscaling of Areal Data: Application to Daily COVID-19 Incidence Rates.

This paper addresses two common challenges in analyzing spatial epidemiological data, specifically disease incidence rates recorded over small areas: filtering noise caused by small local population sizes and deriving estimates at different spatial scales. Geostatistical techniques, including Poisson kriging (PK), have been used to address these issues by accounting for spatial correlation patterns and neighboring observations in smoothing and changing spatial support. However, PK has a limitation in that it can generate unrealistic rates that are either negative or greater than 100%. To overcome this limitation, an alternative method that relies on soft indicator kriging (IK) is presented. The performance of this method is compared to PK using daily COVID-19 incidence rates recorded in 2020-2021 for each of the 581 municipalities in Belgium. Both approaches are used to derive noise-filtered incidence rates for four different dates of the pandemic at the municipality level and at the nodes of a 1 km spacing grid covering the country. The IK approach has several attractive features: (1) the lack of negative kriging estimates, (2) the smaller smoothing effect, and (3) the better agreement with observed municipality-level rates after aggregation, in particular when the original rate was zero.

Determination of combined sibship indices using 15 STR loci and a grey zone in a small local population in central Bosnia and Herzegovina

Determination of combined sibship indices using 15 STR loci and a grey zone in a small local population in central Bosnia and Herzegovina

Molecular-genetics analysis of 15 STR loci in sibship testing in isolated rural Bosnian population - the use of the grey zone.

Aim Examination of the effectiveness of STR loci in proving sibship of the Bosnian-Herzegovinian village of Orahovica and the formation of a "grey zone". Methods The probability of sibship was determined by calculating the likelihood ratio (LR) parameter for each of the 15 observed STR loci and for each of the pairs of relatives and non-relatives. Cumulative sibship index (CSI) was calculated for each of the pairs by multiplying the LR values of all 15 loci and obtained values are used as CSI limit for separating relatives from non-relatives. By creating a grey zone for local populations, an attempt was made to obtain a line of demarcation between siblings and non-siblings. Results An analysis of the origin of the respondents' relatives was performed, up to the level of sibship in the third generation. The results of the CSI for pairs of relatives from the village of Orahovica showed that the highest CSI value, and therefore the sibship probability was recorded among relatives from the village of Orahovica (CSI=534211727.203;SP=99.999999812%). On the contrary, incredibly low CSI value was recorded among non-relatives,ranging from CSI=0.0000001 to 0.5261434 (SP=0.000009999% to 34.475357951%). Conclusion For the threshold value CSI=1 and for CSI=3, this method determined sibship in 100% of pairs of relatives and the absence of biological sibship in 100% of pairs of non-relatives in the village of Orahovica. The STR system is proved to be a successful method in determining sibship or absence of sibship in small local populations.

Eco-evolutionary extinction and recolonization dynamics reduce genetic load and increase time to extinction in highly inbred populations.

Understanding how genetic and ecological effects can interact to shape genetic loads within and across local populations is key to understanding ongoing persistence of systems that should otherwise be susceptible to extinction through mutational meltdown. Classic theory predicts short persistence times for metapopulations comprising small local populations with low connectivity, due to accumulation of deleterious mutations. Yet, some such systems have persisted over evolutionary time, implying the existence of mechanisms that allow metapopulations to avoid mutational meltdown. We first hypothesize a mechanism by which the combination of stochasticity in the numbers and types of mutations arising locally (genetic stochasticity), resulting local extinction, and recolonization through evolving dispersal facilitates metapopulation persistence. We then test this mechanism using a spatially and genetically explicit individual-based model. We show that genetic stochasticity in highly structured metapopulations can result in local extinctions, which can favor increased dispersal, thus allowing recolonization of empty habitat patches. This causes fluctuations in metapopulation size and transient gene flow, which reduces genetic load and increases metapopulation persistence over evolutionary time. Our suggested mechanism and simulation results provide an explanation for the conundrum presented by the continued persistence of highly structured populations with inbreeding mating systems that occur in diverse taxa.

Highlighted articles for February 2022

Highlighted articles for February 2022

Atlantic herring (Clupea harengus) population structure in the Northeast Atlantic Ocean

The Atlantic herring Clupea harengus L has a vast geographical distribution and a complex population structure with a few very large migratory units and many small local populations. Each population has its own spawning ground and/or time, thereby maintaining their genetic integrity. Several herring populations migrate between common feeding grounds and over-wintering areas resulting in frequent mixing of populations. Thus, many herring fisheries are based on mixed populations of different demographic status. In order to avoid overexploitation of weak populations and to conserve biodiversity, understanding the population structure and population mixing is important for maintaining biologically sustainable herring fisheries. The aim of this study was to investigate the genetic population structure of herring in the Faroese and surrounding waters, and to develop genetic markers for distinguishing between four herring management units (often called stocks), namely the Norwegian spring-spawning herring (NSSH), Icelandic summer-spawning herring (ISSH), North Sea autumn-spawning herring (NSAH), and Faroese autumn-spawning herring (FASH). Herring from the four stocks were sequenced at low coverage, and single nucleotide polymorphisms (SNPs) were called and used for population structure analysis and individual assignment. An ancestry-informative SNP panel with 118 SNPs was developed and tested on 240 individuals. The results showed that all four stocks appeared to be genetically differentiated populations, but at lower levels of differentiation between FASH and ISSH than the other two populations. Overall assignment rate with the SNP panel was 80.7%, and agreement between the genetic and traditional visual assignment was 75.5%. The NSAH and NSSH samples had the highest assignment rate (100% and 98.3%, respectively) and highest agreement between traditional and genetic assignment methods (96.6% and 94.9%, respectively). The FASH and ISSH samples had substantially lower assignment rates (72.9% and 51.7%, respectively) and agreement between traditional and genetic methods (39.5% and 48.4%, respectively)

A Population Genomic Assessment of Three Decades of Evolution in a Natural Drosophila Population.

Population genetics seeks to illuminate the forces shaping genetic variation, often based on a single snapshot of genomic variation. However, utilizing multiple sampling times to study changes in allele frequencies can help clarify the relative roles of neutral and non-neutral forces on short time scales. This study compares whole-genome sequence variation of recently collected natural population samples of Drosophila melanogaster against a collection made approximately 35 years prior from the same locality—encompassing roughly 500 generations of evolution. The allele frequency changes between these time points would suggest a relatively small local effective population size on the order of 10,000, significantly smaller than the global effective population size of the species. Some loci display stronger allele frequency changes than would be expected anywhere in the genome under neutrality—most notably the tandem paralogs Cyp6a17 and Cyp6a23, which are impacted by structural variation associated with resistance to pyrethroid insecticides. We find a genome-wide excess of outliers for high genetic differentiation between old and new samples, but a larger number of adaptation targets may have affected SNP-level differentiation versus window differentiation. We also find evidence for strengthening latitudinal allele frequency clines: northern-associated alleles have increased in frequency by an average of nearly 2.5% at SNPs previously identified as clinal outliers, but no such pattern is observed at random SNPs. This project underscores the scientific potential of using multiple sampling time points to investigate how evolution operates in natural populations, by quantifying how genetic variation has changed over ecologically relevant timescales.

Individual vocal signatures show reduced complexity following invasion

The manner in which vocal learning is used for social recognition may be sensitive to the social environment. Biological invaders capable of vocal learning are useful for testing this possibility, as invasion alters population size. Some vocal learning species use frequency modulation patterns of acoustic signals for individual recognition. In such species, frequency modulation patterns should be more complex in larger social groups, reflecting greater selection for individual distinctiveness. We used numbers of nests and nest densities as proxies of local population sizes of native range monk parakeets, Myiopsitta monachus , in Uruguay and invasive range populations in the United States. Flock sizes were obtained to estimate maximum social group sizes per range. Supervised machine learning and frequency contours were employed to compare contact call structure between native and invasive range populations, and the effect of urban habitats on call structure was also assessed. Invasive range populations exhibited fewer nests, lower nest densities and smaller maximum flock sizes, which is consistent with a reduction in population size following invasion. Parakeets at invasive range sites also produced contact calls with simpler frequency modulation patterns. Beecher's statistic (HS) revealed reduced individual identity content and fewer possible unique individual signatures in invasive range calls. Simpler individual signatures are consistent with relaxed selection on the complexity of learned calls likely used for individual vocal recognition in the smaller local populations that we identified post-invasion. Frequency modulation patterns were simpler in urban habitats in both ranges, indicating that urban habitats could also alter the social environment and in turn influence the complexity of learned individual signatures. These findings contribute to a growing literature on the use of vocal learning for individual recognition and indicate that vocal learning can be used to produce individual vocal signatures in a manner sensitive to local population size. • Local population and social group size estimates were smaller in the invasive range. • Invasive range parakeets produced calls with simpler individual signatures. • Urban calls had simpler frequency modulation patterns in the native and invasive ranges. • Monk parakeets may use vocal learning for individual vocal recognition.

Herd clustering strategies and corresponding genetic evaluations based on social-ecological characteristics for a local endangered cattle breed.

The accuracy of breeding values strongly depends on the population and herd structure, i.e., the number of animals considered in genetic evaluations and the size of contemporary groups (CGs). Local breeds are usually kept in small-sized family farms under alternative husbandry conditions. For such herd structure, consideration of classical herd or herd-test-day effects in CG modeling approaches implies only a few records per effect level. In consequence, the present study aimed on methodological evaluations of different herd clustering strategies, considering social–ecological and herd characteristics. In this regard, we considered 19 herds keeping cows from the small local population of German Black Pied cattle (Deutsches Schwarzbuntes Niederungsrind; DSN), 10 herds keeping Holstein Friesian (HF) cows and one mixed herd with HF and DSN cows. Herds were characterized for 106 variables, reflecting farm conditions, husbandry practices, feeding regime, herd management, herd fertility status, herd health status and breeding strategies as well as social–ecological descriptors. The variables were input data for different clustering approaches including agglomerative hierarchical clustering (AHC), partition around medoids (PAM), fuzzy clustering (FZC) and a clustering of variables combined with agglomerative hierarchical clustering (CoVAHC). The evaluation criterion was the average silhouette width (ASW), suggesting a CoVAHC application and consideration of four herd clusters (HCs) for herd allocation (ASW of 0.510). HC1 comprised the larger, half organic and half conventional DSN family farms, which generate their main income from milk production. HC2 consisted of small organic DSN family farms where cows are kept in tie stables. HC3 included the DSN sub-population from former East Germany, reflecting the large-scale farm types. The specialized HF herds were well separated and allocated to HC4. Generalized linear mixed models with appropriate link functions were applied to compare test-day and female fertility traits of 5538 cows (2341 DSN and 3197 HF) from the first three lactations among the four HCs. Least squares means for milk, fat and protein yield (Mkg, Fkg and Pkg) significantly differed between HC. The significant differences among the four HCs clearly indicate the influence of varying herd conditions on cow traits. The similarities of herds within HC suggested the application of HCs in statistical models for genetic evaluations for DSN. In this regard, we found an increase of accuracies of estimated breeding values of cows and sires and of heritabilities for milk yield when applying models with herd-cluster-test-day or herd-cluster-test-month effects compared to classical herd-test-day models. The identified increase for the number of cows and cow records in CG due to HC effects may be the major explanation for the identified superiority.

Metapopulation genetics of endangered reticulated flatwoods salamanders (Ambystoma bishopi) in a dynamic and fragmented landscape

The reticulated flatwoods salamander (Ambystoma bishopi), an endangered species endemic to the longleaf-pine savanna ecosystem of the southeastern U.S., persists in a small number of remnant habitat patches. Breeding ponds and associated populations are threatened by habitat loss, degradation, and fragmentation stemming from fire suppression and land conversion. Understanding influences on population dynamics and genetic diversity will help inform recovery efforts for this and other pond-breeding amphibians. We used 9 microsatellite loci to characterize population structure, migration, and genetic diversity of juvenile (larvae and metamorphs) A. bishopi (n = 607) sampled from thirteen breeding ponds across two breeding seasons. Temporal genetic variation between annual cohorts was minimal compared to spatial variation among locations. The primary genetic subdivision was between two regional groups of breeding ponds (i.e. metapopulations), which were located more than 10 km from each other. Yet even within metapopulations, genetic isolation-by-distance was pronounced, and estimated migration rates among ponds separated by > 400 m were very low. Genetic diversity was positively correlated with the area of suitable breeding habitat in a pond and negatively correlated with distance to other occupied ponds. The effective number of breeders typically was < 30 individuals per year per pond, and all populations showed signs of having been through a severe demographic bottleneck. Small and variable local population sizes suggest the importance of metapopulation dynamics among ponds for maintaining regional persistence and genetic diversity. Such dynamics may be easily disrupted for A. bishopi, so maintaining and restoring connectivity appears crucial for long-term conservation.

Successful rearing of Ostrea edulis from parents originating from the Wadden Sea, the Netherlands

Since 2017, the European flat oyster (Ostrea edulis) reappeared in the Wadden Sea after decades of absence. In several countries, restoration and reinforcement projects have been initiated. Better insight in Ostrea behaviour is needed to ensure sustainable conservation in the future. In order to acquire substantial numbers of oysters for eco-physiological and transplant experiments without threatening the small local population, indoor rearing facilities were set-up at Royal NIOZ. Here, a broodstock of 38 adults originating from the western Wadden Sea, produced over 21 million larvae in 10 batches within 3 months (Sept-Nov 2018). Release of larvae and rearing took place at a water temperature of 19.7 ± 0.6 °C and a salinity of 30.5 ± 0.5 PSU. Outbreaks of Vibrio bacteria did not occur. The growth rate before settlement was 1.5–1.7 μm per day, which was at the low end of growth rates reported in previous studies. The first competent larvae were observed 17–22 days after release. Size at settlement varied between 255−325 μm. Survival until settlement was 0.96−0.98 per day. After settlement, growth rates increased to 30−47 μm per day, with batches that were released in September having a significantly higher growth rate and initial size compared to larvae that were released later. Mortality from release to the end of the experiment (Feb 2019) was 0.04−0.05 per day. A cryopreservation trial did not result in living larvae after thawing, most likely due to their advanced development when preserved. The larvae and juveniles were negatively tested for the parasite Bonamia ostrea and can thus be used in oyster conservation and restoration projects. Recommendations for future breeding attempts include the use of a higher water temperature and slightly higher food concentrations.

Time‐traveling larvae ensure survival in small, synchronously fluctuating populations

AbstractPopulation structure is an important aspect of patchily distributed organisms. Small local populations, large temporal fluctuations, synchronized dynamics, and low migration rates should all lead to lowered rates of patch occupancy and increased extinction risks. These effects can, however, be counteracted if there is a pool of hidden, dormant individuals bridging unfavorable periods. Prolonged diapause—a dormancy that extends over two or more years—provides such a temporal bridge among insects, but its role in structuring patchy populations is poorly known. Based upon a long‐term study, we explore the landscape scale population structure of a galling insect, the larva of which has an unusually long diapause spent hidden in the soil. Gall populations in patches fluctuated synchronously in a long wave with a tenfold amplitude. Abundances were very low with a median of less than twenty galls per patch. Although only a third of the patches had galls in all years, local populations persisted thanks to the pool of diapausing larvae. Colonizations of two new plant patches were very slow. The combination of small, synchronously fluctuating gall populations and high occupancy rates can be maintained because of the very low extinction rates imposed by the time‐traveling diapausing larvae.

Ten principles for conservation translocations of threatened wood-inhabiting fungi

Abstract Unlike for many other organism groups, conservation translocations of fungi are still rare. Encouraged by recent successful translocations, there is a growing interest in applying this conservation tool to threatened wood-inhabiting fungi. When combined with other conservation or restoration measures, translocation can be an effective measure for preventing further population decline in the short term, and species extinctions in the long term. Translocations can be appropriate for rare and specialist fungal species that occur as small local populations in isolated patches across fragmented landscapes, where there is a low likelihood of successful dispersal between distant host trees that have special qualities and are situated in suitable conditions. As species translocations are a controversial topic, the pros and cons of translocation as a conservation tool for threatened fungi need careful consideration. We highlight the uncertainties and risks that are connected to fungal translocations, and propose ten principles adhering to the precautionary principle.

Assessing the buffer effect of floaters by reinforcing local colonization in spatially structured populations

AbstractEcological theory and recent empirical studies show that the persistence of spatially structured populations – those composed of spatially separated local populations connected by dispersal – may require the maintenance of pools of floaters (nonbreeding but sexually mature individuals) that rescue small local populations from extinction by replacing the lost breeders. Regardless of the rescue of local breeding populations, the persistence of spatially structured populations may also depend on sufficient numbers of colonizations that counteract local extinctions. Given their intrinsic potential mobility, floaters have been proposed to promote the persistence of spatially structured populations by enhancing the (re)colonization of empty habitat patches in fragmented habitats. However, robust empirical assessments of this hypothesis are lacking. Using a long‐term woodpecker study in fragmented habitats as a model framework, we addressed the largely neglected hypothesis that floaters enhance the colonization of local patches and, consequently, facilitate the persistence of spatially structured populations. The size of the entire spatially structured system (number of local populations) increased across years due to a slightly higher number of colonizations than extinctions, suggesting that an increase in colonization may enhance the long‐term persistence of this spatially structured population. After controlling for the number of patches occupied in previous years, the number of colonizations was positively related to the number of patches with floaters in previous seasons. Moreover, after controlling for potential confounding factors, patches with floaters were considerably more likely to be colonized in subsequent seasons than patches without floaters (0.079 vs. 0.008). Colonizations were often conducted through inter‐patch dispersal by floaters that established their territory in empty patches after a variable wandering period, which frequently led to delayed breeding beyond the age of sexual maturity. Altogether, these results provide empirical support for the hypothesis of an enhanced colonization mediated by floaters as a buffer mechanism for the long‐term persistence of spatially structured populations.