Different Degrees Of Isolation Research Articles

Lone male loser? Effects of spatial isolation on male pairing success in the Ortolan Bunting (Emberiza hortulana)

Cover photo: Male Ortolan Bunting. Photo: Frode Falkenberg. In small, isolated or fragmented bird populations, past studies have shown that there can be a high proportion of unpaired males. Low male pairing success is suggested to be the result of female-biased natal dispersal and low female recruitment. Indirect evidence indicates that such an effect operates among populations with different degrees of isolation, but little is known of how isolation affects male pairing success within populations. The Norwegian population of Ortolan Buntings (Emberiza hortulana) is distributed in about 50 discrete patches in an area of nearly 500 km2. In this study, we examined whether patch isolation and individual male isolation affected male pairing success. The population has a strongly male-biased sex ratio, with almost half of all males being unpaired. We found that male pairing successs was negatively related to isolation of patches and isolation of individual males in most analyses, and with significant effects in particular in some analyses of individual isolation. Patch population size was measured as the total number of males observed in a particular patch in a specific year and did not have an effect on male pairing success, and was not related to patch isolation. Even though some tests were statistically significant, the magnitude of effects were small and there was large variance in male pairing success. Variance in success suggests that other factors than isolation such as male age or experience may be just as important for male fitness within our study population. Furthermore, we suggest that small effects of isolation were due to the ability of Ortolan Buntings to move large distances within the breeding season, and that isolation effects on small spatial scales are more likely for species with restricted dispersal, such as resident species or species with high population density.

Pollinator distribution in patches of suitable habitat depends more on patch isolation than on floral abundance

Intrinsic complexity of real-world systems makes particularly difficult to decipher which factors influence the dispersal of pollinators in the landscape matrix and their distribution amongst patches of suitable habitat. Saltmarshes are an ideal and naturally simplified landscape to study the ability of different groups of pollinators to disperse across a landscape matrix, as they consist of a matrix of flooded areas surrounding patches of suitable habitat with different degrees of isolation from the mainland and different levels of floral abundance. We hypothesise that pollinator distribution to flowering plants depends more on patch isolation than on floral abundance, with pollinator richness and visitation rates to flowering plants decreasing with increasing distance from the mainland. To this end, we established 60 permanent plots at varying distances from the mainland and monitored pollinator visitation to entomophilous plants. We also quantified the reproductive success of entomophilous species in the surveyed plots by calculating fruit set. We found that the pollinator community of saltmarshes consisted only of flying pollinators with good dispersal abilities, while we recorded no flightless pollinator species. Both pollinator richness and visitation rate decreased with increasing distance of patches of suitable habitat from the mainland, affecting reproductive success of a non-autogamous entomophilous species. Interestingly, floral abundance did not affect pollinator richness and visitation rate to flowering plants, nor did it affect reproductive success of target plant species. In saltmarshes, the pollinator distribution depends more on patch distance from the mainland than on floral abundance. Our results suggest that the presence of patches of suitable habitat in a landscape matrix does not necessarily ensure the maintenance of pollinators. Rather, our results suggest that suitable habitat isolation is the critical factor in pollinator dispersal and distribution that should be considered to improve landscape matrix permeability to pollinators.

Whole-genome resequencing confirms reproductive isolation between sympatric demes of brown trout (Salmo trutta) detected with allozymes.

The sympatric existence of genetically distinguishable populations of the same species remains a puzzle in ecology. Coexisting salmonid fish populations are known from over 100 freshwater lakes. Most studies of sympatric populations have used limited numbers of genetic markers making it unclear if genetic divergence involves certain parts of the genome. We returned to the first reported case of salmonid sympatry, initially detected through contrasting homozygosity at a single allozyme locus (coding for lactate dehydrogenase A) in brown trout in the small Lakes Bunnersjöarna, Sweden. First, we verified the existence of the two coexisting demes using a 96-SNP fluidigm array. We then applied whole-genome resequencing of pooled DNA to explore genome-wide diversity within and between these demes; nucleotide diversity was higher in deme I than in deme II. Strong genetic divergence is observed with genome-wide FST ≈0.2. Compared with data from populations of similar small lakes, this divergence is of similar magnitude as that between reproductively isolated populations. Individual whole-genome resequencing of two individuals per deme suggests higher inbreeding in deme II versus deme I, indicating different degree of isolation. We located two gene-copies for LDH-A and found divergence between demes in a regulatory section of one of these genes. However, we did not find a perfect fit between the sequence data and previous allozyme results, and this will require further research. Our data demonstrates genome-wide divergence governed mostly by genetic drift but also by diversifying selection in coexisting populations. This type of hidden biodiversity needs consideration in conservation management.

Phylogeographic structuring of plastome diversity in Mediterranean oaks (Quercus Group Ilex, Fagaceae)

Oaks of Quercus Group Ilex are emblematic components of the Mediterranean landscapes and the full extent of their diversity in a geographic context is still poorly assessed. In order to detail differentiation patterns within Group Ilex and to illuminate causes and circumstances that underlie the distribution of its lineages, we examined plastome differentiation in the four species currently representing this oak group across the Mediterranean Basin (Quercus ilex, Quercus coccifera, Quercus aucheri, Quercus alnifolia). Plastid DNA variation was explored with three markers on 124 individuals and spatial analyses were performed with phylogenetic and landscape genetics approaches. A strong geographic sorting, entirely decoupled from species boundaries, was found. Spatial coincidences with phylogenetic splits highlights the presence of four geographic regions (the Middle East, the Aegean region, the central and the western Mediterranean) characterised by different degrees of isolation. Distinct sub-regional structures were identified. Inter- and intra-lineage divergence patterns appear to reflect the complex orogeny of the Mediterranean region and Pleistocene climatic oscillations, while a few widespread haplotypes might represent the remnants of the ancestral Group Ilex range. Regional differentiation in this group is recognised to be triggered by a number of factors, including disruption of the original range, incomplete lineage sorting, repeated phases of asymmetrical introgression and isolation. The key role played by some Mediterranean regions on the range establishment and dynamics of this oak group is discussed.

<strong>A case study on the Trichoptera fauna of springs in the escarpment mountains of southern Africa (Insecta, Trichoptera)</strong>

The Trichoptera assemblages of three springs in the escarpment and on the Waterberg of Namibia, and of two springs in the Great Escarpment of South Africa were collected at irregular intervals. The species composition of each spring is presented and discussed in terms of permanence and stability of spring areas. The study has revealed a poor fauna in the Namibian escarpment, which consists of widespread species whereas the springs on the Waterberg and in the Great Escarpment are more speciose and contain relict and possible endemic species as well as widespread and euryoecious species. The differences are due to different degrees of isolation and distance from other freshwater ecosystems and suitable aquatic biotopes in the arid and semiarid environment of southwestern Africa.

The Mass-Dimension Relationships in the Mussels Mytilus Galloprovincialis (Mollusca, Bivalvia) from Different Phenotypical Groups in Periphyton Populations near Odessa Coast, the North-Western Part of Black Sea

Abstract The data of the size-mass indices in the mussels Mytilus galloprovincialis (Lamarck, 1819) from three phenotypic groups - brown, dark violet (black) and “zebra” (brown with radial black stripes) shells in the periphyton settlements on the concrete traverses near Odessa coast, the North-western part of Black Sea (Ukraine), in March-November 2014-2015 are presented. A comparative evaluation has been made on the relationships of total mass of the mollusks, wet and dry mass of their soft body and mass of the shells on the one hand, and the size of animals (length of its shells) on the other hand, in the each of phenotypical groups from the five marine beach areas. It is shown, that in the marine areas with different degrees of isolation from the open sea by coast-protection engineering constructions, the mussels from different phenotypes have almost the same size-mass characteristics. Only the dry weight of soft animal body, which indicated to fatness of mollusk and therefore demonstrated his biological prosperity in specific hydrological conditions, can serve as a reliable criterion which can mark the shellfish habitats with different gradients of environmental factors.

Serenading for Ten Thousand Years: The Mating Call of Insular Populations of the Green TreefrogAplastodiscus Eugenioi(Anura: Hylidae)

Islands are natural laboratories for evolutionary studies due to their small areas, structural complexity (compared to continents), and their different degrees of isolation. The present study involved four distinct areas, one continental and three insular, on the southern coast of the State of Rio de Janeiro, Brazil. These islands were formed by coastal flooding at the end of the last glacial maximum, approximately 10 thousand years ago. We investigated acoustic parameters in the advertisement call of the green tree frog, Aplastodiscus eugenioi (Hylidae), looking for variations that could be associated with geographic isolation in the insular populations. We measured six acoustic parameters of the advertisement calls of 59 males, 15 specimens from the continent and 44 from the islands. We found significant variation in acoustic parameters within the population from ***Ilha de Itacuruca, suggesting that isolation, despite the relatively short period, favored differentiation of acoustical parameters. In fac...

Geographical isolation and genetic differentiation: the case ofOrestias ascotanensis(Teleostei: Cyprinodontidae), an Andean killifish inhabiting a highland salt pan

Orestias ascotanensis is a killifish endemic to the Ascotan salt pan in the Chilean Altiplano, where it inhabits 12 springs with different degrees of isolation. This species is a suitable model for studying the effect of serial geographical isolations on the differentiation process among populations. The present study examines the genetic variation and structure of the species using mitochondrial DNA control region sequences and eight microsatellite loci, analyzing populations across its distribution range. The evaluation of genetic variation revealed high levels of diversity within the species. The genetic structure analysis showed the existence of four differentiated groups: two groups were formed by the springs located in the northern and southern extremes of the salt pan and two groups were found in the centre of the salt pan. The latter two groups were formed by several springs, most likely as a consequence of the South American summer monsoon that could connect them and allow gene flow. The patterns of genetic differentiation appear to be determined based on the physical isolation of the populations. This isolation may be the result of a combination of factors, including geographical distance, a historical decrease in water levels and altitude differences in the springs of the salt pan. Therefore, this system is a rare example in which hydrological factors can explain genetic differentiation on a very small scale.

Would protecting tropical forest fragments provide carbon and biodiversity cobenefits under REDD+?

Tropical forests store vast amounts of carbon and are the most biodiverse terrestrial habitats, yet they are being converted and degraded at alarming rates. Given global shortfalls in the budgets required to prevent carbon and biodiversity loss, we need to seek solutions that simultaneously address both issues. Of particular interest are carbon-based payments under the Reducing Emissions from Deforestation and Forest Degradation (REDD+) mechanism to also conserve biodiversity at no additional cost. One potential is for REDD+ to protect forest fragments, especially within biomes where contiguous forest cover has diminished dramatically, but we require empirical tests of the strength of any carbon and biodiversity cobenefits in such fragmented systems. Using the globally threatened Atlantic Forest landscape, we measured above-ground carbon stocks within forest fragments spanning 13 to 23 442 ha in area and with different degrees of isolation. We related these stocks to tree community structure and to the richness and abundance of endemic and IUCN Red-listed species. We found that increasing fragment size has a positive relationship with above-ground carbon stock and with abundance of IUCN Red-listed species and tree community structure. We also found negative relationships between distance from large forest block and tree community structure, endemic species richness and abundance, and IUCN Red-listed species abundance. These resulted in positive congruence between carbon stocks and Red-listed species, and the abundance and richness of endemic species, demonstrating vital cobenefits. As such, protecting forest fragments in hotspots of biodiversity, particularly larger fragments and those closest to sources, offers important carbon and biodiversity cobenefits. More generally, our results suggest that macroscale models of cobenefits under REDD+ have likely overlooked key benefits at small scales, indicating the necessity to apply models that include finer-grained assessments in fragmented landscapes rather than using averaged coarse-grained cells.

Individual and among-population variation in dispersal-related traits in Natterjack toads

Recent publications on animal conservation called out the need to account for individual and among-population differences in dispersal. Despite the demonstrated links between personality traits and dispersal behavior, most studies of local adaptation have focused on dispersal capacity through variation in morphology and physiology. Ephemeral habitat patches generally favor dispersal capacity, whereas loss and increasing isolation of the patches can select against dispersal capacity. In this study, we explore whether populations of Natterjack toads (Bufo calamita) have evolved different morphologies, physiological performance and personality traits in response to the spatial arrangement of their habitat. First, we studied the consistency and intercorrelations of behavioral traits in order to test for the possible existence of personality, which so far has been largely ignored in the study of amphibians. Second, we assessed levels of population differentiation in candidate personality traits and dispersal capacity. The toadlets in this study originated from populations with different degrees of isolation, due to distance from other populations and resistance of the surrounding landscape, and with different dynamics of the subpopulations. We used two cohorts of toadlets, one raised in a common environment and the other collected in the field. We found consistency and correlations between the behavioral measurements, suggesting the possible existence of personality linked to mobility. The higher locomotor performance in toadlets from the metapopulations in the low-resistance landscape compared with those from the isolated populations indicates local adaptation in dispersal capacity. Yet, we could not demonstrate that differences in behavior can be explained by local adaptation in dispersal-related traits.

Landscape-moderated bird nest predation in hedges and forest edges

Landscape-scale agricultural intensification has caused severe declines in biodiversity. Hedges and forest remnants may mitigate biodiversity loss by enhancing landscape heterogeneity and providing habitat to a wide range of species, including birds. However, nest predation, the major cause of reproductive failure of birds, has been shown to be higher in forest edges than in forest interiors. Little is known about how spatial arrangement (configuration) of hedges affects the avian nest predation. We performed an experiment with artificial ground and elevated nests (resembling yellowhammer and whitethroat nests) baited with quail and plasticine eggs. Nests were placed in three habitat types with different degrees of isolation from forests: forest edges, hedges connected to forests and hedges isolated from forests. Nest predation was highest in forest edges, lowest in hedges connected to forests and intermediate in isolated hedges. In the early breeding season, we found similar nest predation on ground and elevated nests, but in the late breeding season nest predation was higher on ground nests than on elevated nests. Small mammals were the main predators of ground nests and appeared to be responsible for the increase in predation from early to late breeding season, whereas the elevated nests were mainly depredated by small birds and small mammals. High predation pressure at forest edges was probably caused by both forest and open-landscape predators. The influence of forest predators may be lower at hedges, leading to lower predation pressure than in forest edges. Higher predation pressure in isolated than connected hedges might be an effect of concentration of predators in these isolated habitats. We conclude that landscape configuration of hedges is important in nest predation, with connected hedges allowing higher survival than isolated hedges and forest edges.

Environmental diel variation, parasite loads, and local population structuring of a mixed-mating mangrove fish

Genetic variation within populations depends on population size, spatial structuring, and environmental variation, but is also influenced by mating system. Mangroves are some of the most productive and threatened ecosystems on earth and harbor a large proportion of species with mixed-mating (self-fertilization and outcrossing). Understanding population structuring in mixed-mating species is critical for conserving and managing these complex ecosystems. Kryptolebias marmoratus is a unique mixed-mating vertebrate inhabiting mangrove swamps under highly variable tidal regimes and environmental conditions. We hypothesized that geographical isolation and ecological pressures influence outcrossing rates and genetic diversity, and ultimately determine the local population structuring of K. marmoratus. By comparing genetic variation at 32 microsatellites, diel fluctuations of environmental parameters, and parasite loads among four locations with different degrees of isolation, we found significant differences in genetic diversity and genotypic composition but little evidence of isolation by distance. Locations also differed in environmental diel fluctuation and parasite composition. Our results suggest that mating system, influenced by environmental instability and parasites, underpins local population structuring of K. marmoratus. More generally, we discuss how the conservation of selfing species inhabiting mangroves and other biodiversity hotspots may benefit from knowledge of mating strategies and population structuring at small spatial scales.

Patterns of genetic structuring in a brown trout (Salmo trutta L.) metapopulation

One main challenge in conservation biology is to preserve genetic variability and adaptive variation within and among populations. However, constant anthropogenic habitat modifications have severe effects on the evolutionary dynamics shaping wild populations and pose a serious threat to the natural evolution of biodiversity. The aim of the present study was to unravel the genetic structuring of brown trout (Salmo trutta) populations in the largest freshwater catchment in Ireland, whose habitats have experienced major human-mediated changes over at least two centuries. A total of 419 juvenile fish were sampled from nine main rivers in the Corrib catchment and were genotyped using 12 microsatellites. Both Bayesian clustering and FST-based analyses of genetic variance sorted these populations into five main genetically distinct groups, characterized by different extent of genetic differentiation among populations. These groups were also characterized by some degree of admixture, which can be partly explained by recent gene flow. Overall, the study suggests that the Corrib trout may conform to a metapopulation model with local populations that show different degrees of isolation and are interconnected by various level of gene flow. Results add further insights into metapopulation evolutionary dynamics and provide a useful basis to implement appropriate conservation strategies.

Os diferentes graus de isolamento da água subterrânea como origem de sua variabilidade: evidências isotópicas, hidroquímicas e da variação sazonal do nível da água no Pantanal da Nhecolândia

This study aims to analyze the degree of isolation of natural lakes with unusual values of salinity and pH in the area of Pantanal da Nhecolândia, the largest field of lakes in the tropical zone of the planet. This process is still poorly understood and is essential for understanding the entire environment. The salinity was measured by electrical conductivity and shows great variations. The possibility of important variability of evaporation or precipitation was dismissed because the lakes are in the same area and the region is flat. Therefore, salinity differences may be associated with a present processes, provided by different degrees of isolation between the lakes and the groundwater, or originated from salt deposits formed in the past, under arid climate. To test the first hypothesis, we analyzed the ratios of stable isotopes of oxygen and deuterium, since the isotopic fractionation that occurs during evaporation enriches the liquid phase in 18O and D. The correlation between the ratios and electrical conductivity is exponential, indicating that the salinity increases with the isolation of the lakes from the groundwater and that a significant isolation of the lakes results in salinities ranging from intermediate to high. The study presents data on seasonal variation in water level (July 2008, end of rainy season and October 2008, end of dry season) of 14 lakes. The data show erratic decrease in the water level of fresh water lakes, which was interpreted as evidence of greater exchange of water between these lakes and the groundwater.

Phenotypic Diversity of <I>Triatoma infestans</I> at the Microgeographic Level in the Gran Chaco of Argentina and the Andean Valleys of Bolivia

Triatoma infestans (Klug) is the main vector of Trypanosoma cruzi, etiologic agent of Chagas disease. The phenotype of the species varies at different geographic scales. The objective of this study was to compare the antennal phenotype of spatially close T. infestans populations and to evaluate its usefulness as a marker of exchange of individuals between populations. The antennal phenotype of 190 T. infestans from Argentina and Bolivia was analyzed using uni- and multivariate techniques. This study shows heterogeneity of the antennal phenotypes of closely related T. infestans populations living in different habitats. Specimens collected in a goat corral and a rabbit cage in La Rioja (Argentina) were dissimilar to the specimens collected in the nearby intradomestic environment. Similarly, specimens from peridomestic corrals in Cochabamba (Bolivia) were different from the intradomestic and sylvatic specimens, indicating some degree of isolation between these populations. In contrast, T. infestans collected in chicken coops and the intradomestic environment were similar, in all studied regions, suggesting a frequent exchange of individuals between the two habitats and/or because of the similarity of the habitat due to the presence of chickens in the intradomestic environment. We propose that each habitat affects in a particular mode the insect morphology and these changes could be used to identify recolonizing T. infestans. These results support the hypothesis of different degrees of isolation between intradomestic and peridomestic habitats. Within this context, special attention should be given to chicken coops and other close peridomestic structures in relation to the recolonization process of domestic habitats by T. infestans.

Produção de serapilheira em floresta Atlântica secundária numa paisagem fragmentada (Ibiúna, SP): importância da borda e tamanho dos fragmentos

Litter is an important compartment in tropical forests, responsible for most of nutrient cycling. Several environmental factors may affect litter production, and the ones mostly investigated are climate and vegetation structure. The influence of landscape structure on patterns of litter production is poorly studied. This study investigated edge and size effects on patterns of litter production in three Atlantic forest fragments (Ibiuna, SP: 23°35' S - 23°50' S; 46°45' W - 47°15' W), one large (ca. 175 ha) and two small (ca. 5 ha) with different degrees of isolation. The litter collected was fractioned following the predominant plant material, and grouped into two periods, of high and low production. We used analysis of variance and a posteriori tests to detect differences in litter production between edge and center of each fragment, and among the centers of the three fragments. Most biomass consisted of leaves+flowers, followed by twigs < 0.5 cm (62.9% and 24.7% of the total), a common pattern in tropical forests. It was possible to perceive an edge effect related to litter production in the three fragments, especially in the large one, and higher litter production in their centers. The observed patterns showed to be strongly related to the vegetation structure, as the size of trees and canopy density. A higher production of fruits+seeds in the large fragment or in the small and connected one indicate a relationship between forest connectivity and the activity of disperser animals.

The AMIGA sample of isolated galaxies

Context. Studies of the effects of environment on galaxy properties and evolution require well defined control samples. Such isolated galaxy samples have up to now been small or poorly defined. The AMIGA project (Analysis of the interstellar Medium of Isolated GAlaxies) represents an attempt to define a statistically useful sample of the most isolated galaxies in the local (z ≤ 0.05) Universe. Aims. A suitable large sample for the AMIGA project already exists, the Catalogue of Isolated Galaxies (CIG, Karachentseva, 1973, Astrofizicheskie Issledovaniia Izvestiya Spetsial’noj Astrofizicheskoj Observatorii, 8, 3; 1050 galaxies), and we use this sample as a starting point to refine and perform a better quantification of its isolation properties. Methods. Digitised POSS-I E images were analysed out to a minimum projected radius R ≥ 0.5 Mpc around 950 CIG galaxies (those within Vr = 1500 km s −1 were excluded). We identified all galaxy candidates in each field brighter than B = 17.5 with a high degree of confidence using the LMORPHO software. We generated a catalogue of approximately 54 000 potential neighbours (redshifts exist for ≈30% of this sample). Results. Six hundred sixty-six galaxies pass and two hundred eighty-four fail the original CIG isolation criterion. The available redshift data confirm that our catalogue involves a largely background population rather than physically associated neighbours. We find that the exclusion of neighbours within a factor of four in size around each CIG galaxy, employed in the original isolation criterion, corresponds to ∆Vr ≈ 18 000 km s −1 indicating that it was a conservative limit. Conclusions. Galaxies in the CIG have been found to show different degrees of isolation. We conclude that a quantitative measure of this is mandatory. It will be the subject of future work based on the catalogue of neighbours obtained here.

Deslocamentos de morcegos (Mammalia, Chiroptera) em remanescentes de Floresta Atlântica no sul do Brasil

We used mark and recapture techniques to evaluate movements of bats within and between three brazilian forest remnants. We captured bats with mist-nets in four 1 ha plots representing different degrees of isolation of riparian (two plots) and submontane (two plots) forests between July 2002 and June 2003. Using numbered aluminium tags, we marked 635 bats of seven species and 54 individuals of six species were recaptured. Overall, we recaptured Carollia perspicillata (Linnaeus, 1758) (short-tailed fruit bat) most frequently, especially in plots where they were banded in the riparian forest plots. These results suggest that this bat has restricted feeding areas, which are probably determined by the abundance of Piper Linnaeus (Piperaceae), its preferred food item. In contrast, species of the genus Artibeus Leach, 1821 exhibited few recaptures, suggesting high mobility and larger feeding areas. In fact Artibeus seems to use more of the forest remnants in their search for food, especially Ficus Linnaeus (Moraceae), the preferred food of this bat. Our results suggest that even small forest isolates are valuable for the maintenance of some bat species because they offer many of the resources they need or because they are spatially distributed in a pattern that allows use of the entire landscape.

Movements of bats (Mammalia, Chiroptera) in Atlantic Forest remnants in southern Brazil

We used mark and recapture techniques to evaluate movements of bats within and between three brazilian forest remnants. We captured bats with mist-nets in four 1 ha plots representing different degrees of isolation of riparian (two plots) and submontane (two plots) forests between July 2002 and June 2003. Using numbered aluminium tags, we marked 635 bats of seven species and 54 individuals of six species were recaptured. Overall, we recaptured Carollia perspicillata (Linnaeus, 1758) (short-tailed fruit bat) most frequently, especially in plots where they were banded in the riparian forest plots. These results suggest that this bat has restricted feeding areas, which are probably determined by the abundance of Piper Linnaeus (Piperaceae), its preferred food item. In contrast, species of the genus Artibeus Leach, 1821 exhibited few recaptures, suggesting high mobility and larger feeding areas. In fact Artibeus seems to use more of the forest remnants in their search for food, especially Ficus Linnaeus (Moraceae), the preferred food of this bat. Our results suggest that even small forest isolates are valuable for the maintenance of some bat species because they offer many of the resources they need or because they are spatially distributed in a pattern that allows use of the entire landscape.

Migration matrices and surnames in populations with different isolation patterns: Val di Lima (Italian Apennines), Val di Sole (Italian Alps), and La Cabrera (Spain)

Biodemographic methods are widely used to infer the genetic structure of human populations. In this study, we revise and standardize the procedures required by the migration matrix model of Malécot ([1950] Ann Univ Lyon Sci [A] 13:37-60), testing it in large historical-demographic databases of 85 populations from three mountain valleys with different degrees of isolation: Val di Lima (Italian Apennines, 21 parishes), Val di Sole, (Italian Alps, 27 parishes), and La Cabrera (Spain, 37 parishes). An add-on package (Biodem) for the R program is proposed to perform all calculations. Results from migration matrices are compared with those obtained from isonymic relationships. Migration and isonymy matrices are derived from 22,781 marriage records. Matrices are analyzed using a nonlinear isolation-by-distance (IBD) model and multivariate techniques (multidimensional scaling, Procrustes rotation, and cluster analysis). Microdifferentiation levels (F(ST)) from the migration data agree with the observed inbreeding values: higher values are found in La Cabrera (F(ST) = 0.0082), the most isolated population; Val di Lima (F(ST) = 0.0015) and Val di Sole (F(ST) = 0.0012) have lower values due to the larger parish population sizes and greater mobility. Temporal changes of F(ST) and IBD are analyzed using the migration matrix approach. The populations show a marked decline in F(ST) values in time, together with increased population mobility and emigration rates. In all three valleys, marital migration and isonymy yield similar results, suggesting that geographic distance is the most important factor structuring the populations. However, isonymy shows a lower correlation with geographic distance than migration matrices do. This difference can be attributed to the differing sensitivity of the methods for past migration events, and to genetic drift.