Long-term Migration Rates Research Articles

The role of oceanic currents in the dispersal and connectivity of the mangrove Rhizophora mangle on the Southwest Atlantic region.

Dispersal is a crucial mechanism to living beings, allowing them to reach new resources such that populations and species can occupy new environments. However, directly observing the dispersal mechanisms of widespread species can be costly or even impractical, which is the case for mangrove trees. The influence of ocean currents on mangrove dispersal is increasingly evident; however, few studies mechanistically relate the patterns of population distribution with the dispersal by oceanic currents under an integrated framework. Here, we evaluate the role of oceanic currents on connectivity of Rhizophora mangle along the Southwest Atlantic. We inferred population genetic structure and migration rates, simulated the displacement of propagules and tested our hypotheses with Mantel tests and redundancy analysis. We observed populations structured in two major groups, north and south, which is corroborated by other studies with Rhizophora and other coastal plants. Inferred recent migration rates do not indicate ongoing gene flow between sites. Conversely, long-term migration rates were low across groups and contrasting dispersal patterns within each one, which is consistent with long-distance dispersal events. Our hypothesis tests suggest that both isolation by distance and isolation by oceanography (derived from the oceanic currents) can explain the neutral genetic variation of R. mangle in the region. Our findings expand current knowledge of mangrove connectivity and highlight how the association of molecular methods with oceanographic simulations improve the interpretation of the dispersal process. This integrative approach is a cost- and time-efficient strategy to include dispersal and connectivity data into marine protected areas planning and management.

Defining Species When There is Gene Flow.

Whatever one's definition of species, it is generally expected that individuals of the same species should be genetically more similar to each other than they are to individuals of another species. Here, we show that in the presence of cross-species gene flow, this expectation may be incorrect. We use the multispecies coalescent model with continuous-time migration or episodic introgression to study the impact of gene flow on genetic differences within and between species and highlight a surprising but plausible scenario in which different population sizes and asymmetrical migration rates cause a genetic sequence to be on average more closely related to a sequence from another species than to a sequence from the same species. Our results highlight the extraordinary impact that even a small amount of gene flow may have on the genetic history of the species. We suggest that contrasting long-term migration rate and short-term hybridization rate, both of which can be estimated using genetic data, may be a powerful approach to detecting the presence of reproductive barriers and to define species boundaries.[Gene flow; introgression; migration; multispecies coalescent; species concept; species delimitation.].

Population structure and coalescence in pedigrees: Comparisons to the structured coalescent and a framework for inference

Contrary to what is often assumed in population genetics, independently segregating loci do not have completely independent ancestries, since all loci are inherited through a single, shared population pedigree. Previous work has shown that the non-independence between gene genealogies of independently segregating loci created by the population pedigree is weak in panmictic populations, and predictions made from standard coalescent theory are accurate for populations that are at least moderately sized. Here, we investigate patterns of coalescence in pedigrees of structured populations. We find that the pedigree creates deviations away from the predictions of the structured coalescent that persist on a longer timescale than in the case of panmictic populations. Nevertheless, we find that the structured coalescent provides a reasonable approximation for the coalescent process in structured population pedigrees so long as migration events are moderately frequent and there are no migration events in the recent pedigree of the sample. When there are migration events in the recent sample pedigree, we find that distributions of coalescence in the sample can be modeled as a mixture of distributions from different initial sample configurations. We use this observation to motivate a maximum-likelihood approach for inferring migration rates and mutation rates jointly with features of the pedigree such as recent migrant ancestry and recent relatedness. Using simulation, we show that our inference framework accurately recovers long-term migration rates in the presence of recent migration events in the sample pedigree.

Male and Female Subpopulations of Salix viminalis Present High Genetic Diversity and High Long-Term Migration Rates between Them.

Dioecy distributed in 157 flowering plant families and 959 flowering plant genera. Morphological and physiological differences between male and female plants have been studied extensively, but studies of sex-specific genetic diversity are relatively scarce in dioecious plants. In this study, 20 SSR loci were employed to examine the genetic variance of male subpopulations and female subpopulations in Salix viminalis. The results showed that all of the markers were polymorphic (Na = 14.15, He = 0.7566) and workable to reveal the genetic diversity of S. viminalis. No statistically significant difference was detected between male and female subpopulations, but the average genetic diversity of male subpopulations (Na = 7.12, He = 0.7071) and female subpopulations (Na = 7.31, He = 0.7226) were high. Under unfavorable environments (West Liao basin), the genetic diversity between male and female subpopulations was still not significantly different, but the genetic diversity of sexual subpopulations were lower. The differentiation of the ten subpopulations in S. viminalis was moderate (FST = 0.0858), which was conformed by AMOVA that most of genetic variance (94%) existed within subpopulations. Pairwise FST indicated no differentiation between sexual subpopulations, which was accompanied by high long-term migrate between them (M = 0.73~1.26). However, little recent migration was found between sexual subpopulations. Therefore, artificial crossing or/and transplantation by cutting propagation should be carried out so as to increase the migration during the process of ex situ conservation.

Population structure of red snapper (Lutjanus campechanus) in U.S. waters of the western Atlantic Ocean and the northeastern Gulf of Mexico

Population structure of adult red snapper (Lutjanus campechanus) from the southeastern coast of the United States (Atlantic) and the northeastern Gulf of Mexico (Gulf) was assessed using genotypes at 16 nuclear-encoded microsatellites and mitochondrial (mt)DNA haplotypes of the NADH dehydrogenase 4 (ND4) gene. Initial tests (FST-based, hierarchical AMOVA) of spatial genetic homogeneity within and between regions were non-significant, consistent with a single population or stock of red snapper in the Atlantic and Gulf. Inferences derived from other statistical approaches were consistent with genetic and/or demographic differences within and between the two regions. The estimated, average, long-term migration rate between the two regions (0.27%) was well less than the 10% rate below which populations can respond independently to environmental perturbation. Comparisons of global estimates of average, long-term effective size (NeLT) with estimates from individual sample localities indicated genetic heterogeneity within both the Atlantic and Gulf. These results paralleled those of prior genetic studies of red snapper from the Gulf. Future genetics studies and other work on red snapper in both the Atlantic and Gulf should include approaches to identify demographically independent units within each region and assess their size, patterns of connectivity, and contribution to the fishery. Monitoring global and/or local effective size also should be considered.

Global diversity and oceanic divergence of humpback whales (Megaptera novaeangliae).

Humpback whales (Megaptera novaeangliae) annually undertake the longest migrations between seasonal feeding and breeding grounds of any mammal. Despite this dispersal potential, discontinuous seasonal distributions and migratory patterns suggest that humpbacks form discrete regional populations within each ocean. To better understand the worldwide population history of humpbacks, and the interplay of this species with the oceanic environment through geological time, we assembled mitochondrial DNA control region sequences representing approximately 2700 individuals (465 bp, 219 haplotypes) and eight nuclear intronic sequences representing approximately 70 individuals (3700 bp, 140 alleles) from the North Pacific, North Atlantic and Southern Hemisphere. Bayesian divergence time reconstructions date the origin of humpback mtDNA lineages to the Pleistocene (880 ka, 95% posterior intervals 550-1320 ka) and estimate radiation of current Northern Hemisphere lineages between 50 and 200 ka, indicating colonization of the northern oceans prior to the Last Glacial Maximum. Coalescent analyses reveal restricted gene flow between ocean basins, with long-term migration rates (individual migrants per generation) of less than 3.3 for mtDNA and less than 2 for nuclear genomic DNA. Genetic evidence suggests that humpbacks in the North Pacific, North Atlantic and Southern Hemisphere are on independent evolutionary trajectories, supporting taxonomic revision of M. novaeangliae to three subspecies.

Does mating behaviour affect connectivity in marine fishes? Comparative population genetics of two protogynous groupers (Family Serranidae)

Pelagic larval duration (PLD) has been hypothesized to be the primary predictor of connectivity in marine fishes; however, few studies have examined the effects that adult reproductive behaviour may have on realized dispersal. We assessed gene flow (connectivity) by documenting variation in microsatellites and mitochondrial DNA sequences in two protogynous species of groupers, the aggregate spawning red hind, Epinephelus guttatus, and the single-male, harem-spawning coney, Cephalopholis fulva, to ask whether reproductive strategy affects connectivity. Samples of both species were obtained from waters off three islands (Puerto Rico, St. Thomas and St. Croix) in the Caribbean Sea. Despite the notion that aggregate spawning of red hind may facilitate larval retention, stronger signals of population structure were detected in the harem-spawning coney. Heterogeneity and/or inferred barriers, based on microsatellites, involved St. Croix (red hind and coney) and the west coast of Puerto Rico (coney). Heterogeneity and/or inferred barriers, based on mitochondrial DNA, involved St. Croix (coney only). Genetic divergence in both species was stronger for microsatellites than for mitochondrial DNA, suggesting sex-biased dispersal in both species. Long-term migration rates, based on microsatellites, indicated asymmetric gene flow for both species in the same direction as mean surface currents in the region. Red hind had higher levels of variation in microsatellites and lower levels of variation in mitochondrial DNA. Long-term effective size and effective number of breeders were greater for red hind; estimates of θ(f) , a proxy for long-term effective female size, were the same in both species. Patterns of gene flow in both species appear to stem in part from shared aspects of larval and adult biology, local bathymetry and surface current patterns. Differences in connectivity and levels of genetic variation between the species, however, likely stem from differences in behaviour related to reproductive strategy.

Riverbank migration and island dynamics of the braided Jamuna River of the Ganges–Brahmaputra basin using multi-temporal Landsat images

As one of the largest braided rivers in the world, the Jamuna River (JM) of the lower Brahmaputra regularly undergoes significant erosion, causing major bankline migration, making thousands of families homeless and sizeable land loss every year, e.g., the dynamic nature of Jamuna causes great suffering to the people living along its course and on its islands. Therefore, gaining a better understanding of the river's behavior should contribute to mitigate these sufferings and also to reduce the possible damage of the river to public infrastructure. In this study, using thirteen selected images of Landsat MSS and TM acquired from 1973 to 2003, the riverbank migration patterns and island dynamics of JM resulted from accretion/erosion processes for 30 years were investigated. For short-term analysis, the migration rate from one Landsat image to the next is estimated. For long-term analysis, the migration rates are based on the difference between the 1973 image as the reference, and subsequent images. For the short-term (long-term) analysis, the average erosion and accretion rates are 227 and 271 m/y (90 and 104 m/y) on the left bank, and 187 and 148 m/y (75 and 50 m/y) on the right bank of Jamuna, respectively. Because of human interventions and the averaging effect of erosion and accretion, the long-term migration rate is lower than that of the short-term migration rate on both banks. The short-term rate of accretion (erosion) on the left (right) bank follows the general pattern of river bank migration, while the accretion (erosion) of the right (left) bank does not follow such a pattern. On the other hand, the long-term erosion and accretion processes for both banks partly follow the general pattern of river bank migrations. From one flood to another, large islands tend to be more stable with little changes, but smaller islands underwent more changes. From results obtained from analyzing multi-temporal Landsat images, this study provides new and accurate information about the riverbank migration of JM.

Patterns of hybridization and asymmetrical gene flow in hybrid zones of the rare Eucalyptus aggregata and common E. rubida.

The patterns of hybridization and asymmetrical gene flow among species are important for understanding the processes that maintain distinct species. We examined the potential for asymmetrical gene flow in sympatric populations of Eucalyptus aggregata and Eucalyptus rubida, both long-lived trees of southern Australia. A total of 421 adults from three hybrid zones were genotyped with six microsatellite markers. We used genealogical assignments, admixture analysis and analyses of spatial genetic structure and spatial distribution of individuals, to assess patterns of interspecific gene flow within populations. A high number of admixed individuals were detected (13.9-40% of individuals), with hybrid populations consisting of F(1) and F(2) hybrids and backcrosses in both parental directions. Across the three sites, admixture proportions were skewed towards the E. aggregata genetic cluster (x=0.56-0.65), indicating that backcrossing towards E. aggregata is more frequent. Estimates of long-term migration rates also indicate asymmetric gene flow, with higher migration rates from E. aggregata to hybrids compared with E. rubida. Taken together, these results indicate a greater genetic input from E. aggregata into the hybrid populations. This asymmetry probably reflects differences in style lengths (E. rubida: ~7 mm, E. aggregata: ~4 mm), which can prevent pollen tubes of smaller-flowered species from fertilizing larger-flowered species. However, analyses of fine-scale genetic structure suggest that localized seed dispersal (<40 m) and greater clustering between hybrid and E. aggregata individuals may also contribute to directional gene flow. Our study highlights that floral traits and the spatial distributions of individuals can be useful predictors of the directionality of interspecific gene flow in plant populations.

Genome scan of hybridizing sunflowers from Texas (Helianthus annuusandH. debilis) reveals asymmetric patterns of introgression and small islands of genomic differentiation

Although the sexual transfer of genetic material between species (i.e. introgression) has been documented in many groups of plants and animals, genome-wide patterns of introgression are poorly understood. Is most of the genome permeable to interspecific gene flow, or is introgression typically restricted to a handful of genomic regions? Here, we assess the genomic extent and direction of introgression between three sunflowers from the south-central USA: the common sunflower, Helianthus annuus ssp. annuus; a near-endemic to Texas, Helianthus debilis ssp. cucumerifolius; and their putative hybrid derivative, thought to have recently colonized Texas, H. annuus ssp. texanus. Analyses of variation at 88 genetically mapped microsatellite loci revealed that long-term migration rates were high, genome-wide and asymmetric, with higher migration rates from H. annuus texanus into the two parental taxa than vice versa. These results imply a longer history of intermittent contact between H. debilis and H. annuus than previously believed, and that H. annuus texanus may serve as a bridge for the transfer of alleles between its parental taxa. They also contradict recent theory suggesting that introgression should predominantly be in the direction of the colonizing species. As in previous studies of hybridizing sunflower species, regions of genetic differentiation appear small, whether estimated in terms of FST or unidirectional migration rates. Estimates of recent immigration and admixture were inconsistent, depending on the type of analysis. At the individual locus level, one marker showed striking asymmetry in migration rates, a pattern consistent with tight linkage to a Bateson-Dobzhansky-Muller incompatibility.

Fine-scale genetic structure in Ethiopian wolves imposed by sociality, migration, and population bottlenecks

We used demographic, spatial, and microsatellite data to assess fine-scale genetic structure in Ethiopian wolves found in the Bale Mountains and evaluated the impact of historical versus recent demographic processes on genetic variation. We applied several analytical methods, assuming equilibrium and nonequilibrium conditions, to assess demography and genetic structure. Genetic variation (H E = 0.584–0.607, allelic richness = 4.2–4.3) was higher than previously reported for this species and genetic structure was influenced by geography and social structure. Statistically significant F ST values (0.06–0.08) implied differentiation among subpopulations. STRUCTURE analyses showed that neighbouring packs often have shared co-ancestry and spatial autocorrelation showed higher genetic similarity between individuals within packs and between individuals in neighbouring packs compared to random pairs of individuals. Recent effective population sizes were lower than 2n (where n is the number of packs) and lower than the number of breeding individuals with N e /N ratios near 0.20. All subpopulations have experienced bottlenecks, one occurring due to a rabies outbreak in 2003. Nevertheless, differentiation among these subpopulations is consistent with long-term migration rates and fragmentation at the end of the Pleistocene. Enhanced drift due to population bottlenecks may be countered by higher migration into disease-affected subpopulations. Contemporary factors such as social structure and population bottlenecks are clearly influencing the level and distribution of genetic variation in this population, which has implications for its conservation.

Population structure and genetic variation of lane snapper (Lutjanus synagris) in the northern Gulf of Mexico

Lane snappers (Lutjanus synagris), sampled from eight localities in the northern Gulf of Mexico (Gulf) and one locality along the Atlantic coast of Florida, were assayed for allelic variation at 14 nuclear-encoded microsatellites and for sequence variation in a 590 base-pair fragment of the mitochondrially encoded ND-4 gene (mtDNA). Significant heterogeneity among the nine localities in both microsatellite allele and genotype distributions and mtDNA haplotype distributions was indicated by exact tests and by analysis of molecular variance (AMOVA). Exact tests between pairs of localities and spatial analysis of molecular variance (SAMOVA) for both microsatellites and mtDNA revealed two genetically distinct groups: a Western Group that included six localities from the northwestern and northcentral Gulf and an Eastern Group that included three localities, one from the west coast of Florida, one from the Florida Keys, and one from the east (Atlantic) coast of Florida. The between-groups component of molecular variance was significant for both microsatellites (ΦCT = 0.016, P = 0.009) and mtDNA (ΦCT = 0.208, P = 0.010). Exact tests between pairs of localities within each group and spatial autocorrelation analysis did not reveal genetic heterogeneity or an isolation-by-distance effect among localities within either group. MtDNA haplotype diversity was significantly less (P < 0.0001) in the Western Group than in the Eastern Group; microsatellite allelic richness and gene diversity also were significantly less in the Western Group (P = 0.015 and 0.013, respectively). The difference in genetic variability between the two groups may reflect reduced effective population size in the Western Group and/or asymmetric rates of genetic migration. The relative difference in variability between the two groups was substantially greater in mtDNA and may reflect one or more mtDNA selective sweeps; tests of neutrality of the mtDNA data were consistent with this possibility. Bayesian analysis of genetic demography indicated that both groups have experienced a historical decline in effective population size, with the decline being greater in the Western Group. Maximum-likelihood analysis of microsatellite data indicated significant asymmetry in average, long-term migration rates between the two groups, with roughly twofold greater migration from the Western Group to the Eastern Group. The difference in mtDNA variability and the order-of-magnitude difference in genetic divergence between mtDNA and microsatellites may reflect different demographic events affecting mtDNA disproportionately and/or a sexual and/or spatial bias in gene flow and dispersal. The spatial discontinuity among lane snappers in the region corresponds to a known zone of vicariance in other marine species. The evidence of two genetically distinct groupings (stocks) has implications for management of lane snapper resources in the northern Gulf.

Examining the physical meaning of the bank erosion coefficient used in meander migration modeling

Widely used models of meander evolution relate migration rate to vertically averaged near-bank velocity through the use of a coefficient of bank erosion ( E). In applications to floodplain management problems, E is typically determined through calibration to historical planform changes, and thus its physical meaning remains unclear. This study attempts to clarify the extent to which E depends on measurable physical characteristics of the channel boundary materials using data from the Sacramento River, California, USA. Bend-average values of E were calculated from measured long-term migration rates and computed near-bank velocities. In the field, unvegetated bank material resistance to fluvial shear ( k) was measured for four cohesive and noncohesive bank types using a jet-test device. At a small set of bends for which both E and k were obtained, we discovered that variability in k explains much of the variability in E. The form of this relationship suggests that when modeling long-term meander migration of large rivers, E depends largely on bank material properties. This finding opens up the possibility that E may be estimated directly from field data, enabling prediction of meander migration rates for systems where historical data are unavailable or controlling conditions have changed. Another implication is that vegetation plays a limited role in affecting long-term meander migration rates of large rivers like the Sacramento River. These hypotheses require further testing with data sets from other large rivers.

Seeing ghosts: the effect of unsampled populations on migration rates estimated for sampled populations

In 2004, the term 'ghost population' was introduced to summarize the effect of unsampled subpopulations that exchange migrants with other subpopulations that have been sampled. Estimated long-term migration rates among populations sampled will be affected by ghost populations. Although it would be convenient to be able to define an apparent migration matrix among sampled populations that incorporate the exchange of migrants with ghost populations, no such matrix can be defined in a way that predicts all features of the coalescent process for the true migration matrix. This paper shows that if the underlying migration matrix is symmetric, it is possible to define an apparent migration matrix among sampled subpopulations that predicts the same within-population and between-population homozygosities among sampled populations as is predicted by the true migration matrix. Application of this method shows that there is no simple relationship between true and apparent migration rates, nor is there a way to place an upper bound on the effect of ghost populations. In general, ghost populations can create the appearance of migration between subpopulations that do not actually exchange migrants. Comparison with published results from the application of the program, MIGRATE, shows that the apparent migration rates inferred with that program in a three-subpopulation model differ from those based on pairwise homozygosities. The apparent migration matrix determined by the method described in this paper probably represents the upper bound on the effect of ghost populations.

The morphology and migration of transverse bars off the west-central Florida coast

A series of migrating shore-normal sandbars with wavelengths of 75–120 m and heights up to 2 m have been identified off the northern tip of Anna Maria Island, a barrier island on the west-central Florida coast. Similar features have been described elsewhere since the 1930s and termed ‘transverse bars’. The transverse bars identified off Anna Maria Island are found for about 3 km along the coast and extend 4 km offshore, well outside the normal surf-zone width. No cusps or any other associated beach expression is evident despite the fact that the bars come to within about 75 m of the beach. Sediments on the crests of the bars are a well-sorted fine quartz sand, whereas sediments in the troughs are a poorly sorted coarse carbonate shell hash. Historical aerial photographs and repeated high-resolution bathymetric surveys provide a means of quantifying the migration of the transverse bars. Analyses of orthorectified aerial photographs from the early 1940s through the mid 1990s clearly show movement or migration taking place in the bar field. In the 40-yr period from 1951 to 1991, the southern edge of the bar field moved 200–350 m to the south, with an average long-term migration rate of 8 m/yr. Repeated bathymetric surveys over an 8-month period give an average short-term migration rate of 21 m/yr to the south. Wave and current measurements suggest that southerly winds associated with the passage of cold fronts drive near-bed currents to the south that are strong enough to initiate sediment transport and cause the southerly migration of the transverse bars.

Population structure of nuclear and mitochondrial DNA variation among humpback whales in the North Pacific.

The population structure of variation in a nuclear actin intron and the control region of mitochondrial DNA is described for humpback whales from eight regions in the North Pacific Ocean: central California, Baja Peninsula, nearshore Mexico (Bahia Banderas), offshore Mexico (Socorro Island), southeastern Alaska, central Alaska (Prince Williams Sound), Hawaii and Japan (Ogasawara Islands). Primary mtDNA haplotypes and intron alleles were identified using selected restriction fragment length polymorphisms of target sequences amplified by the polymerase chain reaction (PCR-RFLP). There was little evidence of heterogeneity in the frequencies of mtDNA haplotypes or actin intron alleles due to the year or sex composition of the sample. However, frequencies of four mtDNA haplotypes showed marked regional differences in their distributions (phi ST = 0.277; P < 0.001; n = 205 individuals) while the two alleles showed significant, but less marked, regional differences (phi ST = 0.033; P < 0.013; n = 400 chromosomes). An hierarchical analysis of variance in frequencies of haplotypes and alleles supported the grouping of six regions into a central and eastern stock with further partitioning of variance among regions within stocks for haplotypes but not for alleles. Based on available genetic and demographic evidence, the southeastern Alaska and central California feeding grounds were selected for additional analyses of nuclear differentiation using allelic variation at four microsatellite loci. All four loci showed significant differences in allele frequencies (overall FST = 0.043; P < 0.001; average n = 139 chromosomes per locus), indicating at least partial reproductive isolation between the two regions as well as the segregation of mtDNA lineages. Although the two feeding grounds were not panmictic for nuclear or mitochondrial loci, estimates of long-term migration rates suggested that male-mediated gene flow was several-fold greater than female gene flow. These results include and extend the range and sample size of previously published work, providing additional evidence for the significance of genetic management units within oceanic populations of humpback whales.