Quantifying gene flow from spatial genetic structure data in a metapopulation of Chamaecrista fasciculata (Leguminosae)

Abstract An extensive allozyme survey was conducted within a natural "meta" population of the native North American annual legume, Chamaecrista fasciculata (Leguminosae) to quantify genetic structure at different spatial scales. Gene flow was then estimated by a recently developed indirect method based on a continuous population model, using pairwise kinship coefficients between individuals. The indirect estimates of gene flow, quantified in terms of neighborhood size, with an average value on the order of 150 individuals, were concordant among different spatial scales (subpopulation, population, metapopulation). This gene-flow value lies within the range of direct estimates previously documented from observations of pollen and seed dispersal for the same metapopulation. Monte Carlo simulations using the direct measures of gene flow as parameters further demonstrated that the observed spatial pattern of allozyme variation was congruent with a model of isolation by distance. Combining previously published estimates of pollen dispersal distances with kinship coefficients from this study, we quantified biparental inbreeding relative to either a single subpopulation or the whole metapopulation. At the level of a neighborhood, little biparental inbreeding was observed and most departure from Hardy-Weinberg genotypic proportions was explained by self-fertilization, whereas both selfing and biparental inbreeding contributed to nonrandom mating at the metapopulation level. Gene flow was also estimated from indirect methods based on a discontinuous population structure model. We discuss these results with respect to the effect of a patchy population structure on estimation of gene flow.     

A multi-locus assessment of connectivity and historical demography in the bluehead wrasse (Thalassoma bifasciatum)

The pelagic larval stage of most coral reef fishes might allow extensive dispersal or, alternatively, some level of local recruitment might be important. Molecular markers can be used to obtain indirect estimates of dispersal to evaluate these alternatives, yet the extent of gene flow among populations is known for only a small number of species. The use of such markers must take into account the properties of the markers and the demographic history of the population when making inferences about current gene flow. In the Caribbean bluehead wrasse, Thalassoma bifasciatum, previous studies have found both substantial levels of local recruitment, in studies interpreting otolith microchemistry and, conversely, a lack of genetic differentiation inferred from mitochondrial DNA (mtDNA) restriction-fragment length polymorphism (RFLP) data and allozymes. However, if subtle differentiation exists, larger sample sizes and highly variable markers may be required to discern it. Here we present results from mitochondrial control region sequence and microsatellite data that indicate a lack of genetic differentiation at both small and large spatial scales. However, historical processes, such as changes in population size, may have affected the current distribution of genetic variation.     

The genetic effective size of a metapopulation

The structure of a population over time, space and categories of social and sexual role governs its ability to retain genetic variation in the face of drift. A metapopulation is an extreme form of spatial structure in which loosely coupled local populations 'turnover', that is, suffer extinction followed by recolonization from elsewhere within the metapopulation. These local populations turn over with a characteristic half-life. Based on a simulation model that incorporates both realistic features of population ecology and population genetics, the ability of such a metapopulation to retain genetic variation, which may be defined as proportional to its so-called effective population size, denoted N_e(^meta), can be one to two orders of magnitude lower than the maximum total number of individuals in the system. N_e(meta) depends on the persistence time associated with longevity of local populations (the turnover half-life), the average number of local populations extant in the metapopulation and the gene flow between local populations. Habitat fragmentation, which can create a metapopulation from a formerly continuously distributed species, may have unappreciated large genetic consequences for species impacted by human development.     

Identification of metapopulation dynamics among Northern Goshawks of the Alexander Archipelago, Alaska, and Coastal British Columbia

Northern Goshawks occupying the Alexander Archipelago, Alaska, and coastal British Columbia nest primarily in old-growth and mature forest, which results in spatial heterogeneity in the distribution of individuals across the landscape. We used microsatellite and mitochondrial data to infer genetic structure, gene flow, and fluctuations in population demography through evolutionary time. Patterns in the genetic signatures were used to assess predictions associated with the three population models: panmixia, metapopulation, and isolated populations. Population genetic structure was observed along with asymmetry in gene flow estimates that changed directionality at different temporal scales, consistent with metapopulation model predictions. Therefore, Northern Goshawk assemblages located in the Alexander Archipelago and coastal British Columbia interact through a metapopulation framework, though they may not fit the classic model of a metapopulation. Long-term population sources (coastal mainland British Columbia) and sinks (Revillagigedo and Vancouver islands) were identified. However, there was no trend through evolutionary time in the directionality of dispersal among the remaining assemblages, suggestive of a rescue–effect dynamic. Admiralty, Douglas, and Chichagof island complex appears to be an evolutionarily recent source population in the Alexander Archipelago. In addition, Kupreanof island complex and Kispiox Forest District populations have high dispersal rates to populations in close geographic proximity and potentially serve as local source populations. Metapopulation dynamics occurring in the Alexander Archipelago and coastal British Columbia by Northern Goshawks highlight the importance of both occupied and unoccupied habitats to long-term population persistence of goshawks in this region.     

Patterns of differentiation among wild rabbit populations Oryctolagus cuniculus L. in arid and semiarid ecosystems of north-eastern Australia

Feral rabbit populations in Australia have generally been managed using localized control procedures. While these procedures may result in local extinctions, persistence of populations will depend on the probability of recolonization. Genetic markers developed using temperature gradient gel electrophoresis (TGGE) combined with heteroduplex analysis (HA) of mitochondrial DNA (mtDNA) were used to characterize the degree of subdivision and extent of gene flow within and among rabbit populations distributed over large distances (up to 1000 km) in southern Queensland (QLD) and north-west New South Wales (NSW), Australia. TGGE analyses revealed significant heterogeneity in mtDNA control region haplotype frequencies. From heterogeneity χ² tests, it was evident that the differentiation observed was largely attributable to five sites which were located in the semiarid eastern region, whereas haplotype frequencies were homogeneous throughout the arid western region. These results suggest that there are independent population systems within the study area. The extent of gene flow among local populations within each system is related to the spatial configuration of acceptable habitat patches and the persistence of the populations is determined by the probability of recolonization following local extinction. These data suggest that to provide better overall control of rabbit populations, different management strategies may be necessary in arid and semiarid ecosystems. In arid south-west QLD and north-west NSW, where extensive gene flow occurs over large distances, rabbit populations should be managed at a regional level. In semiarid eastern QLD, where gene flow is restricted and populations are more isolated, localized control procedures may provide effective short-term relief. These results indicate that in nonequilibrium systems with patchy distribution of individuals, the interpretation of migration rate from estimates of gene flow obtained using existing genetic models must include an understanding of the spatial and temporal scales over which population processes operate.     

Population genetic structure of Sorex unguiculatus and Sorex caecutiens (Soricidae, Mammalia) in Hokkaido, based on microsatellite DNA polymorphism

We investigated the genetic structure of Sorex unguiculatus and Sorex caecutiens populations in Hokkaido, Japan, using hypervariable microsatellite DNA markers. We used five microsatellite loci to type 475 S. unguiculatus individuals from 20 localities on the Hokkaido mainland and four localities from each of four offshore islands (and 11 shrews from one locality in southern Sakhalin for a particular analysis). We used six microsatellite loci to type 240 S. caecutiens individuals from 13 localities on the Hokkaido mainland. Genetic variation was high in mainland populations of both species and low in the island populations of S. unguiculatus. Allelic richness and island size were positively correlated for S. unguiculatus, suggesting that genetic drift occurred on those islands due to small population size. In addition, four insular populations of S. unguiculatus were genetically differentiated from the mainland populations, although clear phylogeographic clustering was not confirmed among populations on the Hokkaido mainland for either S. unguiculatus or S. caecutiens. Heterozygosity excess was observed in more than half of the populations including the mainland populations of the two species, suggesting recent bottleneck events in these populations. Population dynamics of the shrews might be explained by a metapopulation scheme. According to autocorrelation analysis, the extent of non-random spatial genetic structure was approximately 100 km. Isolation by distance was observed in S. unguiculatus, but not in S. caecutiens although there is a positive trend. The lack of correlation for S. caecutiens might have been due to small sample size. Thus, no obvious differences in population genetic structure were found between the two species on the Hokkaido mainland in the present study, while previous investigations using mitochondrial DNA sequences inferred that these two species might have rather different biogeographic histories.     

Genetic variation and island biogreography: Microsatellite and mitochondrial DNA variation in island populations of the Australian bush rat, Rattus fuscipes greyii

To understand the impact of various factors on the maintenance of genetic variation in natural populations, we need to focus on situations where at least some of these factors are removed or controlled. In this study, we used highly variable, presumably neutral, microsatellite and mtDNA markers to assess the nature of genetic variation in 14 island and two mainland populations of the Australian bush rat, where there is no migration between islands. Thus we are controlling for selection and gene flow. Both marker sets revealed low levels of diversity within the small island populations and extreme differentiation between populations. For six microsatellite loci, all of the small island populations had less genetic variation than the mainland populations; reduction in allelic diversity was more pronounced than loss of heterozygosity. Kangaroo Island, the large island population, had similar levels of diversity to the mainland populations. A 442 base pair (bp) section of the mtDNA control region was screened for variation by outgroup heteroduplex analysis/temperature gradient gel electrophoresis (OHA/TGGE). Only three of the 13 small island populations showed haplotypic diversity: Gambier (2), Waldegrave (2), and Eyere (3). The level of haplotypic diversity in the small island populations was similar to that on the mainland, most likely reflecting a recent population bottleneck on the mainland. In contrast, Kangaroo Island had 9 mtDNA haplotypes. The dominant factor influencing genetic diversity on the islands was island size. No correlation was detected between genetic diversity and the time since isolation or distance form the mainland. The combination of genetic drift within and complete isolation among the small island populations has resulted in rapid and extreme population divergence. Population pair-wise comparisons of allele frequency distributions showed significant differences for all populations for all loci (F _st = 0.11–0.84, R _st = 0.07–0.99). For the mtDNA control region, 92.6% of variation was apportioned between populations; only the Pearson islands shared a haplotype. Mantel tests of pair-wise genetic distance with pair-wise geographic distance showed no significant geographical clustering of haplotypes. However, population substructuring was detected within populations where sampling was conducted over a broader geographical range, as indicated by departures from Hardy-Weinberg equilibrium. Thus substructuring in the ancestral population cannot be ruled out. The dominant evolutionary forces on the islands, after the initial founder event, are stochastic population processes such as genetic drift and mutation. This revised version was published online in July 2006 with corrections to the Cover Date.     

Relative information content of polymorphic microsatellites and mitochondrial DNA for inferring dispersal and population genetic structure in the olive sea snake, Aipysurus laevis

Polymorphic microsatellites are widely considered more powerful for resolving population structure than mitochondrial DNA (mtDNA) markers, particularly for recently diverged lineages or geographically proximate populations. Weaker population subdivision for biparentally inherited nuclear markers than maternally inherited mtDNA may signal male-biased dispersal but can also be attributed to marker-specific evolutionary characteristics and sampling properties. We discriminated between these competing explanations with a population genetic study on olive sea snakes, Aipysurus laevis. A previous mtDNA study revealed strong regional population structure for A. laevis around northern Australia, where Pleistocene sea-level fluctuations have influenced the genetic signatures of shallow-water marine species. Divergences among phylogroups dated to the Late Pleistocene, suggesting recent range expansions by previously isolated matrilines. Fine-scale population structure within regions was, however, poorly resolved for mtDNA. In order to improve estimates of fine-scale genetic divergence and to compare population structure between nuclear and mtDNA, 354 olive sea snakes (previously sequenced for mtDNA) were genotyped for five microsatellite loci. F statistics and Bayesian multilocus genotype clustering analyses found similar regional population structure as mtDNA and, after standardizing microsatellite F statistics for high heterozygosities, regional divergence estimates were quantitatively congruent between marker classes. Over small spatial scales, however, microsatellites recovered almost no genetic structure and standardized F statistics were orders of magnitude smaller than for mtDNA. Three tests for male-biased dispersal were not significant, suggesting that recent demographic expansions to the typically large population sizes of A. laevis have prevented microsatellites from reaching mutation-drift equilibrium and local populations may still be diverging.     

Investigating sex‐specific dynamics using uniparental markers: West New Guinea as a case study

Mitochondrial DNA (mtDNA) and Y chromosome (NRY) genetic markers have been often contrasted to investigate sex‐specific dynamics. Traditionally, isolation by distance, intrapopulation genetic diversity and population differentiation are estimated from both markers and compared. Two possible sources of bias are often neglected. First, kilometric distances are frequently used as predictor of the connectivity between groups, hiding the role played by environmental features at a microgeographic scale. Second, the comparison of intrapopulation diversity and population differentiation between mtDNA and NRY is hampered by their different mutational mechanisms and rates. Here, we show how to account for these biases by analyzing from a different perspective a published dataset of eight West New Guinea (WNG) populations for which mtDNA control region sequences and seven linked NRY microsatellites had been typed. First, we modeled the connectivity among sampled populations by computing the number of days required to travel between groups. Then, we investigated the differences between the two sexes accounting for the molecular characteristics of the markers examined to obtain estimates on the product of the effective population size and the migration rate among demes (Nm). We achieved this goal by studying the shape of the gene genealogy at several sampling levels and using spatial explicit simulations. Both the direction and the rate of migration differ between male and females, with an Nm estimated to be >6 times higher in the latter under many evolutionary scenarios. We finally highlight the importance of applying metapopulation models when analyzing the genetic diversity of a species.     

Demographic and genetic factors shaping contemporary metapopulation effective size and its empirical estimation in salmonid fish

The preservation of biodiversity requires an understanding of the maintenance of its components, including genetic diversity. Effective population size determines the amount of genetic variance maintained in populations, but its estimation can be complex, especially when populations are interconnected in a metapopulation. Theory predicts that the effective size of a metapopulation (meta-N(e)) can be decreased or increased by population subdivision, but little empirical work has evaluated these predictions. Here, we use neutral genetic markers and simulations to estimate the effective size of a putative metapopulation in Atlantic salmon (Salmo salar). For a weakly structured set of rivers, we find that meta-N(e) is similar to the sum of local deme sizes, whereas higher genetic differentiation among demes dramatically reduces meta-N(e) estimates. Interdemic demographic processes, such as asymmetrical gene flow, may explain this pattern. However, simulations also suggest that unrecognized population subdivision can also introduce downward bias into empirical estimation, emphasizing the importance of identifying the proper scale of distinct demographic and genetic processes. Under natural patterns of connectivity, evolutionary potential may generally be maintained at higher levels than the local population, with implications for conservation given ongoing species declines and habitat fragmentation.     

Genetic consequences of human management in an introduced island population of red deer (Cervus elaphus)

We investigated phylogeography and spatial genetic structure in an introduced island population of red deer (Cervus elaphus) on the Isle of Rum, Scotland, experiencing spatial variation in management regime. Five different mitochondrial DNA (mtDNA) haplotypes were present among female red deer on Rum. These comprised two phylogenetically divergent groups, one of which clustered with red deer from Sardinia and North Africa, while the other four grouped with other Western European red deer. Recent and historical red deer management practices explain this result. The Rum population is descended from recent introductions from at least four different UK mainland populations, and translocation of red deer within the UK and across Europe is well documented. We found significant spatial genetic structure across Rum in both mtDNA haplotypes and microsatellite markers. Mitochondrial spatial structure was over an order of magnitude greater than structure in nuclear markers. This extreme difference is explained by the fact that the Rum population was introduced from different source populations, the highly male-biased dispersal patterns of red deer and the much smaller effective population size of mitochondrial compared to nuclear markers. Spatial structure in mtDNA conformed to a pattern of isolation by distance, while nuclear DNA did not. Apparent structure in the nuclear markers was driven by differences between the North Block and the rest of the island. We suggest that recent differences in the management regimes in different parts of the island have led to differences in effective male migration that would account for this observation.     

Phylogeography of the marbled crab Pachygrapsus marmoratus (Decapoda,Grapsidae) along part of the African Mediterranean coast reveals genetic homogeneity across the Siculo-Tunisian Strait versus heterogeneity across the Gibraltar Strait

We investigate the influence of previously postulated biogeographic barriers in the Mediterranean Sea on the population genetic structure of a highly dispersive and continuously distributed coastal species. In particular, we examine nuclear and mitochondrial genetic variation in the marbled crab, Pachygrapsus marmoratus, across part of the African Mediterranean coast in order to assess the influence of the Siculo-Tunisian Strait on its population genetic structure. Four polymorphic microsatellite loci were genotyped for 110 individuals, collected from eight locations covering parts of the Algerian, Tunisian and Libyan coasts. In addition, mtDNA corresponding to the Cox1 gene was sequenced for 80 samples. The corresponding results show contrasting patterns of genetic differentiation. While mtDNA results revealed a homogeneous haplotype composition in our study area, microsatellite data depicted genetic differentiation among populations, but not associated with any geographic barrier. This pattern, already recorded for this species from different geographic regions, may hint at the involvement of a complex series of abiotic and biotic factors in determining genetic structure. Demographic history reconstruction, inferred from mtDNA data, supports demographic and spatial expansion for the North African metapopulation dating back to the Mid-Pleistocene and following an historical bottleneck. Comparison of these African mitochondrial sequences with new sequences from a Turkish population and previously published sequences revealed a weak but significant separation of Atlantic and Mediterranean populations across the Gibraltar Strait, which was not recorded in previous studies of this grapsid species.     

Assessing genetic diversity for conservation management: a case study of a threatened reptile

The consequences of inbreeding in small isolated populations are well documented, yet populations are often managed in isolation to avoid irreversibly mixing genetic lineages and to maintain the historic integrity of each population. Three remaining populations of Whitaker's skink ( Cyclodina whitakeri ) in New Zealand, remnants of a once wider distribution, illustrate the conflict between this genetic goal (separate management of populations) with the more tangible and immediate threats of small population size and inbreeding. Middle and Castle Islands harbour populations of C. whitakeri and have been separated from each other and from the mainland for ∼10 000 years. The single mainland population at Pukerua Bay is extremely small, declining and deemed a high priority for management. We sequenced a 550 bp region of mitochondrial DNA (mtDNA,ND2) and genotyped animals from all three populations at 13 microsatellite loci. The population of C. whitakeri at Pukerua Bay showed marked differences from the island populations at both mtDNA (unique, fixed haplotype) and microsatellite loci ( F _ST∼0.20), and private alleles were detected at a high frequency (24% of all alleles). However, we attribute this pattern to an historic genetic gradient coupled with rapid genetic drift. Further, animals in captivity show genetic signatures of both Pukerua Bay and island populations, despite the goal to maintain a pure Pukerua Bay stock. The mixed genetic stock in captivity provides an opportunity for the addition of skinks from Middle Island to evaluate the risks of further population hybridization, including the disruption of potential local adaptation, while mitigating the risks of inbreeding.     

Long-term temporal changes of genetic composition in brown trout (Salmo trutta L.) populations inhabiting an unstable environment

The genetic structure of brown trout (Salmo trutta) populations inhabiting rivers on the island of Bornholm in the Baltic Sea was studied on a spatial and temporal scale. Low water levels in the rivers during the summer period are assumed to have a significant impact on the persistence of local populations, possibly resulting in a metapopulation structure. Extinctions may, however, also be buffered by a remnant strategy, whereby juveniles escape to river outlets during periods of drought. We compared polymorphism at seven microsatellite DNA loci in contemporary and past samples collected from 1944 to 1997. A principal component analysis, a hierarchical gene diversity analysis and assignment tests showed that the genetic composition of populations was not temporally stable, and that temporal genetic differentiation was much stronger than spatial differentiation. Genetic variability was high and stable over time. Effective population sizes (Ne) and migration rate (m) were estimated using a maximum-likelihood-based implementation of the temporal method. Ne estimates were low (ranging from 8.3 to 22.9) and estimates of m were high (between 0.23 and 0.99), in contrast to other Danish trout populations inhabiting larger and more environmentally stable rivers (Ne between 39.2 and 289.9 and m between 0.01 and 0.09). Thus, the observed spatio-temporal patterns of genetic differentiation can be explained by drift in small persisting populations, where levels of genetic variation are maintained by strong gene flow. However, observations of rivers devoid of trout suggested that population turnover also takes place. We suggest that Bornholm trout represent a metapopulation where the genetic structure primarily reflects strong drift and gene flow, combined with occasional extinction-recolonization events.     

Individual genetic diversity correlates with the size and spatial isolation of natal colonies in a bird metapopulation

The genetic consequences of small population size and isolation are of central concern in both population and conservation biology. Organisms with a metapopulation structure generally show effective population sizes that are much smaller than the number of mature individuals and this can reduce genetic diversity especially in small sized and isolated subpopulations. Here, we examine the association between heterozygosity and the size and spatial isolation of natal colonies in a metapopulation of lesser kestrels (Falco naumanni). For this purpose, we used capture-mark-recapture data to determine the patterns of immigration into the studied colonies, and 11 highly polymorphic microsatellite markers that allowed us to estimate genetic diversity of locally born individuals. We found that individuals born in smaller and more isolated colonies were genetically less diverse. These colonies received a lower number of immigrants, supporting the idea that both reduced gene flow and small population size are responsible for the genetic pattern observed. Our results are particularly intriguing because the lesser kestrel is a vagile and migratory species with great movement capacity and dispersal potential. Overall, this study provides evidence of the association between individual heterozygosity and the size and spatial isolation of natal colonies in a highly mobile vertebrate showing relatively frequent dispersal and low genetic differentiation among local subpopulations.     

Long-distance seed dispersal in a metapopulation of Banksia hookeriana inferred from a population allocation analysis of amplified fragment length polymorphism data

There is currently a poor understanding of the nature and extent of long-distance seed dispersal, largely due to the inherent difficulty of detection. New statistical approaches and molecular markers offer the potential to accurately address this issue. A log-likelihood population allocation test (AFLPOP) was applied to a plant metapopulation to characterize interpopulation seed dispersal. Banksia hookeriana is a fire-killed shrub, restricted to sandy dune crests in fire-prone shrublands of the Eneabba sandplain, southwest Australia. Population genetic variation was assessed for 221 individuals sampled from 21 adjacent dune-crest populations of B. hookeriana using amplified fragment length polymorphism. Genetic diversity was high, with 175 of 183 (96%) amplified fragment length polymorphism markers polymorphic. Of the total genetic diversity, 8% was partitioned among populations by amova and FST. There was no relationship between genetic diversity within populations and population demographic parameters such as population size and sample size. A population allocation test on these data unambiguously assigned 177 of 221 (80.1%) individuals to a single population. Of these, 171 (77.4% of total) were assigned to the population from which they were sampled and 6 (2.7% of total) were assigned to a known population other than the one from which they were sampled. A further 9 (4.1% of total) were assigned to outside the sampled metapopulation area, and 35 individuals (15.8%) could not be assigned unambiguously to any particular population. These results suggest that both the extent [15 of 221 (6.8%) individuals originating from a population other than the one in which they occur] and distance (1.6 to > 2.5 km), of seed dispersal between dune-crest populations is greater than expected from previous studies. The extent of long-distance interpopulation seed dispersal observed provides a basis for explaining the survival of populations of the fire-killed B. hookeriana in a landscape experiencing frequent fire, where local extinctions and recolonizations may be a regular occurrence.     

Population Genetic Structure of the Magnificent Frigatebird Fregata magnificens (Aves,Suliformes) Breeding Colonies in the Western Atlantic Ocean

The Magnificent Frigatebird Fregata magnificens has a pantropical distribution, nesting on islands along the Atlantic and Pacific coasts. In the Caribbean, there is little genetic structure among colonies; however, the genetic structure among the colonies off Brazil and its relationship with those in the Caribbean are unknown. In this study, we used mtDNA and microsatellite markers to infer population structure and evolutionary history in a sample of F. magnificens individuals collected in Brazil, Grand Connétable (French Guyana), and Barbuda. Virtually all Brazilian individuals had the same mtDNA haplotype. There was no haplotype sharing between Brazil and the Caribbean, though Grand Connétable shared haplotypes with both regions. A Bayesian clustering analysis using microsatellite data found two genetic clusters: one associated with Barbuda and the other with the Brazilian populations. Grand Connétable was more similar to Barbuda but had ancestry from both clusters, corroborating its “intermediate” position. The Caribbean and Grand Connétable populations showed higher genetic diversity and effective population size compared to the Brazilian population. Overall, our results are in good agreement with an effect of marine winds in isolating the Brazilian meta-population.     

Genetic influences on social dominance: cow wars

Analyzing population dynamics in changing habitats is a prerequisite for population dynamics forecasting. The recent development of metapopulation modeling allows the estimation of dispersal kernels based on the colonization pattern but the accuracy of these estimates compared with direct estimates of the seed dispersal kernel has rarely been assessed. In this study, we used recent genetic methods based on parentage analysis (spatially explicit mating models) to estimate seed and pollen dispersal kernels as well as seed and pollen immigration in fragmented urban populations of the plant species Crepis sancta with contrasting patch dynamics. Using two independent networks, we documented substantial seed immigration and a highly restricted dispersal kernel. Moreover, immigration heterogeneity among networks was consistent with previously reported metapopulation dynamics, showing that colonization was mainly due to external colonization in the first network (propagule rain) and local colonization in the second network. We concluded that the differences in urban patch dynamics are mainly due to seed immigration heterogeneity, highlighting the importance of external population source in the spatio-temporal dynamics of plants in a fragmented landscape. The results show that indirect and direct methods were qualitatively consistent, providing a proper interpretation of indirect estimates. This study provides attempts to link genetic and demographic methods and show that patch occupancy models may provide simple methods for analyzing population dynamics in heterogeneous landscapes in the context of global change.     

Hierarchical genetic structure and gene flow in three sympatric species of Amazonian rodents

The population genetic structure of three species of Amazonian rodents ( Oligoryzomys microtis, Oryzomys capito , and Mesomys hispidus ) is examined for mtDNA sequence haplotypes of the cytochrome b gene by hierarchical analysis of variance and gene flow estimates based on fixation indices ( N _ST) and coalescence methods. Species samples are from the same localities along 1000 km of the Rio Juruá in western Amazonian Brazil, but each species differs in important life history traits such as population size and reproductive rate. Average haplotype differentiation, hierarchical haplotype apportionment, and gene flow estimates are contrasted in discussing the current and past population structure. Two species exhibit isolation by distance patterns wherein gene flow is largely limited to geographically adjacent localities. Mesomys exhibits this pattern throughout its range along the river. More than 75% of haplotype variation is apportioned among localities and regions, and estimates of Nm for pair-wise comparisons are nearly always less than 1. Oligoryzomys shows weak isolation by distance, but only over the largest geographical distances. Nm values for this species are nearly always above 1 and most (about 80%) of haplotype variation is contained within local populations. In contrast, Oryzomys exhibits no genetic structure throughout its entire distribution; Nm values average 17 and nearly 90% of the total haplotype variance is contained within local populations. Although gene flow estimates are high, the pattern of Nm as a function of geographical distance suggests that this species experienced a more recent invasion of the region and is still in genetic disequilibrium under its current demographic conditions.