A general model of site-dependent population regulation: population-level regulation without individual-level interactions

In this paper, we use a modeling approach to explore the population regulatory consequences of individual choices for where to breed in heterogeneous environments. In contrast to standard models, we focus on individuals that interact only indirectly through their choices of breeding sites (i.e., individuals preempt the occupation of a breeding site by others when they choose to breed there). We consider the consequences of individuals choosing breeding sites either randomly or sequentially from best to worst. Our analysis shows that average per-capita fecundity of the population is independent of the number of occupied breeding sites if individuals choose sites at random and that variation in average per-capita fecundity increases as population size declines. In contrast, if individuals choose breeding sites sequentially from highest to lowest quality, then as population size increases average per-capita fecundity declines and variation in average per-capita fecundity increases. Consequently, aggregate population-level demographic rates can change in ways that generate population regulation, even when change in population size does not change the demographic performance of any individual on any particular breeding site. However, such regulation occurs only when individuals make adaptive choices of where to breed. Because variation in average per-capita fecundity decreases when population size declines, populations regulated in a site-dependent manner should be much less susceptible to the vicissitudes of small population size than those which choose breeding sites at random.     

Fine-scale spatial genetic structure and dispersal among spotted salamander (Ambystoma maculatum) breeding populations

We examined fine-scale genetic variation among breeding aggregations of the spotted salamander (Ambystoma maculatum) to quantify dispersal, interpopulation connectivity and population genetic structure. Spotted salamanders rely on temporary ponds or wetlands for aggregate breeding. Adequate breeding sites are relatively isolated from one another and field studies suggest considerable adult site fidelity; therefore, we expected to find population structure and differentiation at small spatial scales. We used microsatellites to estimate population structure and dispersal among 29 breeding aggregations in Tompkins County, New York, USA, an area encompassing 1272 km(2). Bayesian and frequency-based analyses revealed fine-scale genetic structure with two genetically defined demes: the North deme included seven breeding ponds, and the South deme included 13 ponds. Nine ponds showed evidence of admixture between these two genetic pools. Bayesian assignment tests for detection of interpopulation dispersal indicate that immigration among ponds is common within demes, and that certain populations serve as sources of immigrants to neighbouring ponds. Likewise, spatial genetic correlation analyses showed that populations < or = 4.8 km distant from each other show significant genetic correlation that is not evident at higher scales. Within-population levels of relatedness are consistently larger than expected if mating were completely random across ponds, and in the case of a few ponds, within-population processes such as inbreeding or reproductive skew contribute significantly to differentiation from neighbouring ponds. Our data underscore the importance of these within-population processes as a source of genetic diversity across the landscape, despite considerable population connectivity. Our data further suggest that spotted salamander breeding groups behave as metapopulations, with population clusters as functional units, but sufficient migration among demes to allow for potential rescue and recolonization. Amphibian habitats are becoming increasingly fragmented and a clear understanding of dispersal and patterns of population connectivity for taxa with different ecologies and life histories is crucial for their conservation.     

Seasonal abundance of nonbreeding Piping Plovers on a Georgia barrier island

ABSTRACT.   Although breeding populations of Piping Plovers are well studied, their winter distribution is less clear. We studied the seasonal abundance of nonbreeding Piping Plovers ( Charadrius melodus ) during the winters of 2003–2004 and 2004–2005 on Little St. Simons Island (LSSI), Georgia. Our objectives were to determine the relative abundance of individuals from three breeding populations at LSSI, and identify possible differences among populations in arrival time, winter movements, or departure time. We observed up to 100 Piping Plovers during peak migration, and approximately 40 plovers wintered at LSSI. From July 2004 to May 2005, approximately 20% of the Great Lakes breeding population used LSSI. Plovers were not present at LSSI during June. All breeding populations of Piping Plovers had similar patterns of temporal occurrence on LSSI, suggesting no need for population-specific management plans at this site. Our results suggest that LSSI is among the most important wintering sites on the Atlantic coast for Piping Plovers, especially for individuals from the endangered Great Lakes population.     

A multi-scale analysis of breeding site characteristics of the endangered fire salamander (Salamandra infraimmaculata) at its extreme southern range limit

Understanding species’ distributions often requires taking into consideration the characterization of the environment at different spatial scales. The habitat characteristics of the endangered fire salamander, S. infraimmaculata, have received little attention. In this study, at this species’ most peripheral and xeric limit (Mt. Carmel, Israel), we examined predictors of the larval distribution of S. infraimmaculata at aquatic-breeding sites at both local and landscape scales. We investigated the predictive power of environmental variables using two methods: generalized linear models and conditional inference trees (CTREE). Both multi-model approaches yielded similar results. At the local site scale, hydroperiod predicted breeding site use. At the landscape scale, Salamandra presence was best predicted by proximity to other breeding sites. In addition, our study indicates that sites selected for breeding are far from roads and agricultural fields. Overall, this study demonstrates that ultimately, both local and landscape scale predictors are necessary to understand properly a species’ habitat requirements and thus can help in planning future management around the breeding sites.     

ARTIFICIAL SELECTION FOR PAEDOMORPHOSIS IN THE SALAMANDER AMBYSTOMA TALPOIDEUM

Heterochronic ontogenetic mechanisms such as paedomorphosis are potentially important mechanisms of both microevolutionary and macroevolutionary change. The salamander Ambystoma talpoideum is facultatively paedomorphic. Expression of paedomorphosis in this species varies among local natural populations. Two breeding lines, one from a population associated with a temporary pond where metamorphosis to a terrestrial adult always occurs, another from a population associated with a nearly permanent pond where paedomorphosis is common, were selected artificially for paedomorphosis over four generations. The F₅ generation of each breeding line was reared in a “common garden” field experiment under two drying regimes to simulate the larval environment in a temporary and in a permanent pond. There was a significantly different response to the drying regimes and to the artificial selection in the two lines. A significant population × selection interaction indicated that the two populations responded differently to artificial selection for paedomorphosis. The presence of heritable genetic variation suggests that evolution and divergence among populations of salamanders is possible with intense natural selection over short periods of ecological time.     

Breeding variation in female kakapo (

We investigated why some mature females of New?Zealand?s critically endangered parrot, the kakapo (Strigops habroptilus), did not attempt to breed during the 2005 breeding season on Codfish Island. At a population level, the initiation of kakapo breeding appears to correspond with years of mast fruiting of rimu (Dacrydium cupressinum) trees, with the proportion of females that breed each season dependent on the quantity of rimu fruit available. This research investigates possible links between habitat quality within individual home ranges and the breeding status of adult females during 2005, when the abundance of available rimu fruit was low. We assessed the importance of both home range size and habitat characteristics in determining breeding attempts. Foraging home ranges were characterised using radio-tracking and triangulation techniques. The relative importance of habitat variables in optimal breeding habitat was assessed using ecological niche factor analysis. Our results show that female kakapo breeding in 2005 had, on average, home ranges twice the size of those females that did not breed that season and the ranges contained a significantly greater quantity of mature rimu forest. Multivariate analysis illustrates female kakapo were effectively partitioning available habitat, as breeders? foraging locations were positively correlated with high-abundance rimu forest with a tall canopy, described as optimal breeding habitat. In contrast non-breeders? locations were weakly correlated with short forest containing little or no mature rimu forest. To maximise reproductive output each breeding season, conservation managers need to ensure that all breeding-aged females occupy optimal breeding habitat on Codfish Island. Removal to other islands of kakapo not required in the breeding population may enable females to increase their home range size and occupy better breeding habitat.     

Determinants of size at metamorphosis in an endangered amphibian and their projected effects on population stability

Roughly 80% of animal species have complex life cycles spanning a major habitat shift, and delayed life history effects play an important role in their population dynamics. Through their effect on size at metamorphosis, factors in the pre‐ metamorphic environment often have profound effects upon survival and fecundity in the post‐metamorphic environment. Here, we adopted a combined experimental and field observational approach to investigate the factors that determine size at metamorphosis in pond‐breeding amphibians, and to predict some of their downstream effects on population stability. We set up ecologically realistic mesocosm communities for the endangered California tiger salamander Ambystoma californiense to test the effects of larval density, prey density and hydroperiod on mean size at metamorphosis. We found significant effects for all three factors, with mean size at metamorphosis negatively correlated with larval density and positively correlated with prey density and hydroperiod. We also used six years of field survey data to identify the most informative model explaining mean size at metamorphosis and thus validate our mesocosm results. The optimal three‐term model identified terms that were roughly analogous to each of the mesocosm treatments and with similar effect sizes, providing strong field confirmation of our experimental results. The field data also provide correlations between each factor and the number of metamorphs recruited to the population, allowing us to predict the effect of each factor on population stability. Finally, we show that these populations of the endangered A. californiense are strongly resource limited, which has important implications for their management and recovery as an endangered taxon.     

Food abundance and clutch size of Tree Swallows Tachycineta bicolor

We studied Tree Swallows Tachycineta bicolor during eight breeding seasons (1977-84) at three sites that differed in food availability, which we measured as an index of the biomass of flying insects derived from daily catches in suspended nets. Mean clutch size differed significantly between sites (6.2, 5.8, and 5.6 eggs) and was related to average food abundance at the site. Within two sites, clutch sizes were significantly larger in years when food was more abundant during egg-laying ( r = 0.83 and 0.97 at the high and low food abundance sites, respectively; r = 0.63, not significant, at the medium abundance site). Both clutch size and laying season food abundance were positively correlated with food abundance during the nestling stage at the 'high' site, but not at the other two sites. Our results support the hypothesis that female Tree Swallows respond proximately to abundant food during egg-laying by laying more eggs, but they do not elucidate the ultimate evolutionary factors involved in determining clutch size.     

Abundance patterns of European breeding birds

The frequency distribution of national population sizes of breeding birds was examined for each of 48 European countries, including autonomous regions, using data from the European Bird Database. The frequency distribution of logarithmically transformed abundance was left skewed in 40 countries: there was significant left skew in 10, and positive skew, in 2 countries. The inclusion of data classed as of low quality did not alter the conclusion that abundance patterns were predominantly left skewed. Abundance patterns of resident and migrant breeding birds differed; residents were left skewed, migrants were lognormal. Skewness was correlated negatively the number of species within a country. At low sample size, both left and right skews were evident, but left skews predominated at larger samples sizes. This pattern was driven partly by a difference between breeding populations on islands and on continental countries. Resampling procedures with fixed sample size showed that resident and migrant birds differed consistently in their patterns of skew, independent of sample size. If the birds of Europe were treated as a single assemblage, their abundance pattern was left skewed but this was driven by a very small number of vagrant breeders.     

Large males have a mating advantage in a species of darter with smaller, allopaternal males Etheostoma olmstedi

Theory suggests that males that are larger than their competitors may have increased mating success, due to both greater competitive ability and increased attractiveness to females. We examined how male mating success varies with male size in the tessellated darter Etheostoma olmstedi. Previous work has shown that large males tend to move around and breed in vacant breeding sites, and consequently provide less care for their eggs, while smaller individuals can be allopaternal, caring for the eggs of other males as well as for their own. We studied female egg deposition in a natural breeding population using artificial breeding sites and in the laboratory, where female choice of spawning site was restricted to two breeding sites tended by two males of different sizes. In both the field and the laboratory, nests tended by larger males were more likely to receive new eggs. Additionally, the mean size of males associated with a nest was positively correlated with both the maximum coverage of eggs at the nest and the number of times new eggs were deposited. We discuss how the increased mating success of larger males, despite their decreased parental care, may help explain allopaternal care in this species [Current Zoology 56 (1): 1-5, 2010].     

Inbreeding and genetic structure in the endangered Sorraia horse breed: implications for its conservation and management

The Sorraia horse is a closed breed with reduced effective population size and considered in critical maintained risk status. The breed exists in 2 main breeding populations, one in Portugal and one in Germany, with a smaller population size. A set of 22 microsatellite loci was used to examine genetic diversity and structure of the Sorraia horse breed and to compare individual inbreeding coefficient F, estimated from pedigree data, with individual heterozygosity and mean d(2). The Sorraia horse shows lower levels of microsatellite diversity when compared with other horse breeds. Due to management strategies, there are clear differences in the genetic structure of the 2 main Sorraia horse populations. Individual heterozygosity was shown to be a good estimator, used together with or as an alternative to inbreeding coefficient, in predicting fitness and evaluating the inbreeding level of the Sorraia horse. The information gathered in this study, combined with information available from previous studies, offers an important and wide information base for the future development of an effective breeding management of the Sorraia horse in order to preserve this endangered breed.     

Population and microhabitat effects of interspecific interactions on the endangered Andalusian toothcarp (A<Emphasis Type="Italic">phanius baeticus</Emphasis>)

The Andalusian toothcarp, Aphanius baeticus, is a critically endangered cyprinodontid species, with only nine known extant populations. Although not yet studied in the field, the distribution and abundance of Andalusian toothcarp are thought to be strongly influenced by interspecific interactions. We analysed the abundance and microhabitat use of Andalusian toothcarp in two water courses, one in which several other fish species occurred (sympatric site) and one hypersaline stream in which toothcarp was the only species present (allopatric site). Fish were sampled using plastic minnow traps and results were analysed separately for three size categories. Toothcarps were clearly more abundant in the allopatric population than in the sympatric one, though the difference was less apparent in the smallest size category. In coexistence with other species, toothcarp occupied shallower microhabitats, but in both sites in the absence of shelter fish selected deeper positions than in its absence. While in the sympatric site sheltered microhabitats were used predominately by small individuals, in the allopatric ones they were used by larger ones. Observed patterns strongly suggest that predation is the main mechanism involved in the differences in abundance and microhabitat use between sites. Our results confirm that the presence or absence of coexisting species is an important habitat feature for Andalusian toothcarp populations.     

State uncertainty models and mark‐resight models for understanding non‐breeding site use by Piping Plovers

Conservation of beach‐nesting medium‐distance migrants has focused on breeding areas because protection of nests is more tractable than protection of non‐breeding habitat. As breeding ground management has encountered diminishing returns, interest in understanding threats in non‐breeding areas has increased. However, robust estimates of non‐breeding demographic rates and abundance are generally lacking, hindering the study of limiting factors. Estimating such rates is made more difficult by complex population dynamics at non‐breeding sites. In South Carolina, endangered Piping Plovers Charadrius melodus start arriving in July and some depart prior to December (the autumn‐only population) while others remain through at least March (the wintering population). State uncertainty capture‐mark‐recapture models provide a means for estimating vital rates for such co‐occurring populations. We estimated the proportion of the population entering the study area per survey (entry probability) and proportion remaining per survey (persistence rate) for both populations during autumn, and abundance of the wintering population, at four sites in South Carolina in 2006/7 and 2007/8, taking advantage of birds previously colour‐ringed on the breeding grounds. We made fairly precise estimates of entry and persistence rates with small sample sizes. Cumulative entry probability was ~50% by the end of July and reached 95% for both populations by October. Estimated stopover duration for birds in the autumn‐only population was 35 days in year 1 and 42 days in year 2. We estimated a wintering super‐population size of 71 ± 16 se birds in the first year and 75 ± 16 in the second. If ringing programmes on the breeding grounds continue, standardized resighting surveys in the non‐breeding period and mark‐recapture models can provide robust estimates of entry and persistence rates and abundance. Habitat protection intended to benefit non‐breeding Piping Plovers at our coastal sites should be in effect by late summer, as many birds are resident from July to the end of winter.     

Breeding latitude leads to different temporal but not spatial organization of the annual cycle in a long‐distance migrant

The temporal and spatial organization of the annual cycle according to local conditions is of crucial importance for individuals’ fitness. Moreover, which sites and when particular sites are used can have profound consequences especially for migratory animals, because the two factors shape interactions within and between populations, as well as between animal and the environment. Here, we compare spatial and temporal patterns of two latitudinally separated breeding populations of a trans‐Equatorial passerine migrant, the collared flycatcher Ficedula albicollis, throughout the annual cycle. We found that migration routes and non‐breeding residency areas of the two populations largely overlapped. Due to climatic constraints, however, the onset of breeding in the northern population was approximately two weeks later than that of the southern population. We demonstrate that this temporal offset between the populations carries‐over from breeding to the entire annual cycle. The northern population was consistently later in timing of all subsequent annual events – autumn migration, non‐breeding residence period, spring migration and the following breeding. Such year‐round spatiotemporal patterns suggest that annual schedules are endogenously controlled with breeding latitude as the decisive element pre‐determining the timing of annual events in our study populations.     

Genome-wide analysis in endangered populations: a case study in Barbaresca sheep

Analysis of genomic data is becoming increasingly common in the livestock industry and the findings have been an invaluable resource for effective management of breeding programs in small and endangered populations. In this paper, with the goal of highlighting the potential of genomic analysis for small and endangered populations, genome-wide levels of linkage disequilibrium, measured as the squared correlation coefficient of allele frequencies at a pair of loci, effective population size, runs of homozygosity (ROH) and genetic diversity parameters, were estimated in Barbaresca sheep using Illumina OvineSNP50K array data. Moreover, the breed’s genetic structure and its relationship with other breeds were investigated. Levels of pairwise linkage disequilibrium decreased with increasing distance between single nucleotide polymorphisms. An average correlation coefficient <0.25 was found for markers located up to 50 kb apart. Therefore, these results support the need to use denser single nucleotide polymorphism panels for high power association mapping and genomic selection efficiency in future breeding programs. The estimate of past effective population size ranged from 747 animals 250 generations ago to 28 animals five generations ago, whereas the contemporary effective population size was 25 animals. A total of 637 ROH were identified, most of which were short (67%) and ranged from 1 to 10 Mb. The genetic analyses revealed that the Barbaresca breed tended to display lower variability than other Sicilian breeds. Recent inbreeding was evident, according to the ROH analysis. All the investigated parameters showed a comparatively narrow genetic base and indicated an endangered status for Barbaresca. Multidimensional scaling, model-based clustering, measurement of population differentiation, neighbor networks and haplotype sharing distinguished Barbaresca from other breeds, showed a low level of admixture with the other breeds considered in this study, and indicated clear genetic differences compared with other breeds. Attention should be given to the conservation of Barbaresca due to its critical conservation status. In this context, genomic information may have a crucial role in management of small and endangered populations.     

Genetic diversity and population structure of the Black-faced Spoonbill (Platalea minor) among its breeding sites in South Korea: Implication for conservation

The endangered Black-faced Spoonbill Platalea minor has experienced drastic reductions in population size, geographic distribution, and habitat availability throughout East Asia. In the present study, we examined population genetic structure and genetic diversity of Black-faced Spoonbills inhabiting five sites off the west coast of South Korea encompassing a few of its major breeding sites. Ten microsatellite loci and the mitochondrial sequence were used to assess patterns of genetic variation based on 63 individuals. Three ND2 haplotypes were found among 61 individuals; the remaining two were identified as Eurasian Spoonbills, revealing an unexpected hybridization between these two species having different ecological niches in South Korea—the Eurasian Spoonbill overwinters in inland areas, whereas the Black-faced Spoonbill inhabits coastal areas during the summer. Analyses of microsatellite variation revealed no discrete population structure among the five breeding sites but very weak genetic differentiation among geographically distant regions. Assignment tests identified several possible migrants among sites. Our findings suggested that Black-faced Spoonbills from the five breeding sites could be managed as a single population and highlighted the importance of conserving the populations from Maedo, Suhaam, and Namdong reservoir, which are geographically close and have retained high levels of genetic diversity and large populations.     

Farm‐by‐farm analysis of microsatellite,mtDNA and SNP genotype data reveals inbreeding and crossbreeding as threats to the survival of a native Spanish pig breed

The Chato Murciano (CM), a pig breed from the Murcia region in the southeastern region of Spain, is a good model for endangered livestock populations. The remaining populations are bred on approximately 15 small farms, and no herdbook exists. To assess the genetic threats to the integrity and survival of the CM breed, and to aid in designing a conservation program, three genetic marker systems – microsatellites, SNPs and mtDNA – were applied across the majority of the total breeding stock. In addition, mtDNA and SNPs were genotyped in breeds that likely contributed genetically to the current CM gene pool. The analyses revealed the levels of genetic diversity within the range of other European local breeds (H_e = 0.53). However, when the eight farms that rear at least 10 CM pigs were independently analyzed, high levels of inbreeding were found in some. Despite the evidence for recent crossbreeding with commercial breeds on a few farms, the entire breeding stock remains readily identifiable as CM, facilitating the design of traceability assays. The genetic management of the breed is consistent with farm size, farm owner and presence of other pig breeds on the farm, demonstrating the highly ad hoc nature of current CM breeding. The results of genetic diversity and substructure of the entire breed, as well as admixture and crossbreeding obtained in the present study, provide a benchmark to develop future conservation strategies. Furthermore, this study demonstrates that identifying farm‐based practices and farm‐based breeding stocks can aid in the design of a sustainable breeding program for minority breeds.     

Population-specific adjustment of the annual cycle in a super-swift trans-Saharan migrant

For migratory birds optimal timing of the onset of reproduction is vital, especially when suitable conditions for reproduction occur only for a short while during the year. With increasing latitude the suitable period becomes shorter and we expect the organization of annual cycle to be more synchronized to the local conditions across individuals of same population. This should result in low variation of arrival and departure date in breeding sites at higher latitudes. We quantify the temporal and geographical variation in pre- and post-breeding migration between individuals from four different populations of alpine swifts Tachymarptis melba along a latitudinal gradient. We tracked 215 individuals in three years with geolocators. The two western and two eastern populations showed separate migratory flyways and places of residence in Africa. Length of stay at the breeding sites was negatively correlated with latitude and differed by more than a month between populations. Duration of migration was similarly short in all populations (median 6.2 days in autumn and 8.7 days in spring). However, variation in timing of migration was unrelated to latitude and individuals everywhere arrived in the same asynchrony at the breeding site.     

Population dynamics in migratory networks

Migratory animals are comprised of a complex series of interconnected breeding and nonbreeding populations. Because individuals in any given population can arrive from a variety of sites the previous season, predicting how different populations will respond to environmental change can be challenging. In this study, we develop a population model composed of a network of breeding and wintering sites to show how habitat loss affects patterns of connectivity and species abundance. When the costs of migration are evenly distributed, habitat loss at a single site can increase the degree of connectivity (mixing) within the entire network, which then acts to buffer global populations from declines. However, the degree to which populations are buffered depends on where habitat loss occurs within the network: a site that has the potential to receive individuals from multiple populations in the opposite season will lead to smaller declines than a site that is more isolated. In other cases when there are equal costs of migration to two or more sites in the opposite season, habitat loss can result in some populations becoming segregated (disconnected) from the rest of the network. The geographic structure of the network can have a significant influence on relative population sizes of sites in the same season and can also affect the overall degree of mixing in the network, even when sites are of equal intrinsic quality. When a migratory network is widely spaced and migration costs are high, an equivalent habitat loss will lead to a larger decline in global population size than will occur in a network where the overall costs of migration are low. Our model provides an important foundation to test predictions related to habitat loss in real-world migratory networks and demonstrates that migratory networks will likely produce different dynamics from traditional metapopulations. Our results provide strong evidence that estimating population connectivity is a prerequisite for successfully predicting changes in migratory populations.     

Body size variation of the floodwater mosquito Aedes albifasciatus in Central Argentina

An inverse relationship between larval density and adult body size has been reported for several mosquito species, affecting their survival and vector competence, response to repellents and other factors. Larvae of the floodwater mosquito Aedes (Ochlerotatus) albifasciatus (Macquart) (Diptera: Culicidae) develop quickly in temporary pools, so intraspecific competition (for food or space) might regulate population abundance and affect the size of adult mosquitoes. We investigated the temporal variation of adult female wing-length (an index of body-size) in natural populations of Ae. albifasciatus, using adults collected during each phase of the rainy season. The relationships between adult mosquito abundance, female wing-length, rainfall and temperature were analysed through simple regressions. Skewness of the frequency distribution of wing-lengths showed a strong negative relationship with mean wing-length. The distribution of wing-lengths varied seasonally and was correlated with rainfall 7-15 days previously as the major consequence of breeding site volume. Thus temporal variation of body size in natural populations of Ae. albifasciatus reflected density-dependent changes in the aquatic habitat where immature stages develop, influenced more by rainfall than by temperature or other environmental variables.