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A modified stepping-stone model of population structure in red drum, Sciaenops ocellatus (Sciaenidae), from the northern Gulf of Mexico.

Genetic studies of population or 'stock' structure in exploited marine fishes typically are designed to determine whether geographic boundaries useful for conservation and management planning are identifiable. Implicit in many such studies is the notion that subpopulations or stocks, if they exist, have fixed territories with little or no gene exchange between them. Herein, we review our long-term genetic studies of red drum (Sciaenops ocellatus), an estuarine-dependent sciaenid fish in the Gulf of Mexico and western Atlantic Ocean. Significant differences in frequencies of mitochondrial DNA haplotypes and of alleles at nuclear-encoded microsatellites occur among red drum sampled across the northern Gulf of Mexico. The spatial distribution of the genetic variation, however, follows a pattern of isolation-by-distance consistent with the hypothesis that gene flow occurs among subpopulations and is an inverse (and continuous) function of geographic distance. However, successful reproduction and recruitment of red drum depend on estuarine habitats that have geographically discrete boundaries. We hypothesize that population structure in red drum follows a modified one-dimensional, linear stepping-stone model where gene exchange occurs primarily (but not exclusively) between adjacent bays and estuaries distributed linearly along the coastline. Gene flow does occur among estuaries that are not adjacent but probabilities of gene exchange decrease as a function of geographic distance. Implications of our hypothesis are discussed in terms of inferences drawn from patterns of isolation-by-distance and relative to conservation and management of estuarine-dependent species like red drum. Based on estimates of the ratio of genetic effective population size and census size in red drum, observed patterns of gene flow in red drum may play a significant role in recruitment.

Animals↗

A virus reveals population structure and recent demographic history of its carnivore host.

Directly transmitted parasites often provide substantial information about the temporal and spatial characteristics of host-to-host contact. Here, we demonstrate that a fast-evolving virus (feline immunodeficiency virus, FIV) can reveal details of the contemporary population structure and recent demographic history of its natural wildlife host (Puma concolor) that were not apparent from host genetic data and would be impossible to obtain by other means. We suggest that rapidly evolving pathogens may provide a complementary tool for studying population dynamics of their hosts in "shallow" time.

Alberta↗

Persistence of selfish genetic elements: population structure and conflict.

Selfish genetic elements are vertically transmitted factors that spread by obtaining a transmission advantage relative to the rest of the genome of their host organism, often with a cost to overall host fitness. In many cases, conventional population genetics theory predicts them spreading through populations, reaching fixation and becoming undetectable or sometimes driving the population extinct. However, in several well studied systems, these genetic elements are known to persist at relatively low, stable frequencies. Recent research suggests that several processes might explain these observations, including population structure, intragenomic conflict and coevolution.

Journal Article↗

Human population structure and genetic association studies.

Population substructure and recent admixture may confound the results of genetic association studies in unrelated individuals, leading to a potential excess of both false positive and false negative results. The possibility of false associations depends on the population sampled, the trait being studied and the marker being tested. Although family based tests of association avoid the possibility of confounding due to population substructure and admixture, association studies in unrelated individuals may be preferred in many situations due to their feasibility. Unlinked genetic markers may be used to detect confounding in association studies. In addition, the information from unlinked markers may be used to adjust genetic associations.

Genetic Linkage↗

Genetic variation versus recombination rate in a structured population of mice.

The correlation between genetic variation and recombination rate was investigated in a structured mouse population. Nucleotide sequence data from 19 autosomal DNA loci from eight inbred strains of mouse (Mus musculus) sampled from three major subspecies were analyzed. The recombination rate was estimated from the comparison of genetic and physical map distances between markers flanking a 10-cM region of each locus. The strains were categorized into four groups (subpopulations) based on geography. By partitioning the genetic diversity into within-group and among-group variation, we detected a positive correlation between the recombination rate and nucleotide diversity within groups. The level of nucleotide differentiation among groups (G(ST)) showed a negative correlation with the rate of recombination. There was no significant correlation between recombination rate and nucleotide diversity when data from different subpopulations were pooled. No correlation was detected between recombination rate and nucleotide divergence of M. musculus and M. spicilegus. These patterns deviate from the strict neutral expectation under the constant nucleotide substitution rate, and they are likely to have been formed either by a hitchhiking effect of positively selected mutants or by background selection of deleterious mutants occurring in a subdivided population. Our series of comparisons show that because a real population always has some structure, incorporation of its information is important in detecting non-neutral evolution.

Animals↗

Bathymetric and geographic population structure in the pan-Atlantic deep-sea bivalve Deminucula atacellana (Schenck, 1939).

The deep-sea soft-sediment environment hosts a diverse and highly endemic fauna of uncertain origin. We know little about how this fauna evolved because geographic patterns of genetic variation, the essential information for inferring patterns of population differentiation and speciation are poorly understood. Using formalin-fixed specimens from archival collections, we quantify patterns of genetic variation in the protobranch bivalve Deminucula atacellana, a species widespread throughout the Atlantic Ocean at bathyal and abyssal depths. Samples were taken from 18 localities in the North American, West European and Argentine basins. A hypervariable region of mitochondrial 16S rDNA was amplified by polymerase chain reaction (PCR) and sequenced from 130 individuals revealing 21 haplotypes. Except for several important exceptions, haplotypes are unique to each basin. Overall gene diversity is high (h = 0.73) with pronounced population structure (Phi(ST) = 0.877) and highly significant geographic associations (P < 0.0001). Sequences cluster into four major clades corresponding to differences in geography and depth. Genetic divergence was much greater among populations at different depths within the same basin, than among those at similar depths but separated by thousands of kilometres. Isolation by distance probably explains much of the interbasin variation. Depth-related divergence may reflect historical patterns of colonization or strong environmental selective gradients. Broadly distributed deep-sea organisms can possess highly genetically divergent populations, despite the lack of any morphological divergence.

Animals↗

Successional changes in an evolving anaerobic chlorophenol-degrading community used to infer relationships between population structure and system-level processes.

The response of a complex methanogenic sediment community to 2-chlorophenol (2-CP) was evaluated by monitoring the concentrations of this model contaminant and important metabolic intermediates and products and by using rRNA-targeted probes to track several microbial populations. Key relationships between the evolving population structure, formation of metabolic intermediates, and contaminant mineralization were identified. The nature of these relationships was intrinsically linked to the metabolism of benzoate, an intermediate that transiently accumulated during the mineralization of 2-CP. Before the onset of benzoate fermentation, reductive dehalogenation of 2-CP competed with methanogenesis for endogenous reducing equivalents. This suppressed H(2) levels, methane production, and archaeal small-subunit (SSU)-rRNA concentrations in the sediment community. The concentrations of bacterial SSU rRNA, including SSU rRNA derived from "Desulfovibrionaceae" populations, tracked with 2-CP levels, presumably reflecting changes in the activity of dehalogenating organisms. After the onset of benzoate fermentation, the abundance of Syntrophus-like SSU rRNA increased, presumably because these syntrophic organisms fermented benzoate to methanogenic substrates. Consequently, although the parent substrate 2-CP served as an electron acceptor, cleavage of its aromatic nucleus also influenced the sediment community by releasing the electron donors H(2) and acetate. Increased methane production and archaeal SSU-rRNA levels, which tracked with the Syntrophus-like SSU-rRNA concentrations, revealed that methanogenic populations in particular benefited from the input of reducing equivalents derived from 2-CP.

Acetates↗

[The population structure of agamic protozoan species: Leishmania].

The problem of intraspecific variability in agamic protozoans is analyzed using Leishmania as an example on the basis of data obtained within the last decade using modern methods of molecular biology and biochemistry. We demonstrate local populations resulting from their coevolutionary interaction with other members of the parasitic system: mosquitoes (Diptera, Phlebotominae) and mammals. The existence of a population structure substantiates the notion of species for Leishmania genus; their properties fit within the generally accepted frames of this taxon criterions.

Animals↗

A nonlinear structured population model of tumor growth with quiescence.

A nonlinear structured cell population model of tumor growth is considered. The model distinguishes between two types of cells within the tumor: proliferating and quiescent. Within each class the behavior of individual cells depends on cell size, whereas the probabilities of becoming quiescent and returning to the proliferative cycle are in addition controlled by total tumor size. The asymptotic behavior of solutions of the full nonlinear model, as well as some linear special cases, is investigated using spectral theory of positive simigroup of operators.

Animals↗

Genetic population structure of Natterer's bats explained by mating at swarming sites and philopatry.

During autumn 'swarming', large numbers of temperate bats chase each other in and around underground sites. Swarming has been proposed to be a mating event, allowing interbreeding between bats from otherwise isolated summer colonies. We studied the population structure of the Natterer's bat (Myotis nattereri), a swarming species in northern England, by sampling bats at seven sites in two swarming areas and at 11 summer colonies. Analysis of molecular variance (amova) and genetic assignment analyses showed that the swarming areas (60 km apart) support significantly different populations. A negative correlation was found between the distance of a summer colony from a swarming area and the assignment of bats to that area. High gene diversity was found at all sites (HE = 0.79) suggesting high gene flow. This was supported by a low FST (0.017) among summer colonies and the absence of isolation by distance or substructure among colonies which visit one swarming area. The FST, although low, was significantly different from zero, which could be explained by a combination of female philopatry and male-mediated gene flow through mating at swarming sites with bats from other colonies. Modelling suggested that if effective size of the summer colonies (Ne) was low to moderate (10-30), all mating must occur at the swarming sites to account for the observed FST. If the Ne was higher (50), in addition to random mating during swarming, there may be nonrandom mating at swarming sites or some within-colony mating. Conservation of swarming sites that support potentially large populations is discussed.

Animals↗

Multiclonal Leishmania braziliensis population structure and its clinical implication in a region of endemicity for American tegumentary leishmaniasis.

In Corte de Pedra (CP), northeastern Brazil, Leishmania braziliensis causes three distinct forms of American tegumentary leishmaniasis (ATL). To test the hypothesis that strain polymorphism may be involved in this disease spectrum and accurately characterize the parasite population structure in CP, we compared one L. major, two non-CP L. braziliensis, one CP L. amazonensis, and 45 CP L. braziliensis isolates, obtained over a 10-year period from localized cutaneous, mucosal, and disseminated leishmaniasis patients, with randomly amplified polymorphic DNA (RAPD). Electrophoretic profiles were mostly unique across species. All typing protocols revealed polymorphism among the 45 CP L. braziliensis isolates, which displayed eight different RAPD patterns and greater than 80% overall fingerprint identity, attesting to the adequacy of the tools to assess strain variability in CP's geographically limited population of parasites. The dendrogram based on the sum of RAPD profiles of each isolate unveiled nine discrete typing units clustered into five clades. Global positioning showed extensive overlap of these clades in CP, precluding geographic sequestration as the mechanism of the observed structuralization. Finally, all forms of ATL presented a statistically significant difference in their frequencies among the clades, suggesting that L. braziliensis genotypes may be accompanied by specific disease manifestation after infection.

Animals↗

Optimal sex ratios in structured populations.

In this paper, we develop a general method to determine evolutionary equilibrium sex ratios and to check evolutionary stability, continuous stability and invadability in exact genetic models with or without dominance. This method is then applied to three kinds of models for structured populations: the first one concerns Hamilton's LMC model, except that only a fraction beta of female offspring mate with male offspring born in the same colonies, while a fraction 1-beta mate with male offspring chosen at random within the whole population; in the second model, it is assumed that partial dispersal of inseminated females occurs after mating; in the third model, partial dispersal of male and female offspring occurs before mating. In the first model, the effect of population regulation is studied while, in the other models, two kinds of dispersal are considered: proportional and uniform.

Animals↗

Cryptic population structure in a large, mobile mammalian predator: the Scandinavian lynx.

The Eurasian lynx (Lynx lynx) is an example of a species that has gone through a severe bottleneck, leading to near extinction in Scandinavia around 1930-- a pattern shared with several other large carnivorous mammals. Here we extend previous genetic analyses of northern European lynx, confirming that lynx from the Scandinavian Peninsula represent a distinct clade differing clearly from European conspecifics. Furthermore, and despite a recent bottleneck and subsequent range expansion, we detect marked genetic differentiation within Scandinavia. This differentiation is largely manifested as a north-south gradient, with a linear increase in the quantity FST/(1 - FST). Aided by computer simulations we find that this pattern is unlikely to have arisen by random genetic drift in the short time since lynx started to expand in the 1950s, suggesting that the spatial structure may predate the bottleneck. Individual-based analyses indicate that, instead of a continuous gradient, Scandinavian lynx may be structured into three more or less distinct groups, possibly corresponding to northern, central and southern subpopulations. The presence of such structuring was unknown previously and was unexpected from general considerations on the mobility of the species, historical data and the absence of geographical barriers. Our study demonstrates how molecular markers may be used to detect cryptic population structure, invisible using traditional methods.

Animals↗

RAD-Seq-derived SNPs reveal no local population structure in the commercially important deep-sea queen snapper (Etelis oculatus) in Puerto Rico.

UNLABELLED: The queen snapper (Etelis oculatus Valenciennes in Cuvier & Valenciennes, 1828) is a deep-sea snapper whose commercial importance continues to increase in the US Caribbean. However, little is known about the biology and ecology of this species. In this study, the presence of a fine-scale population structure and genetic diversity of queen snapper from Puerto Rico was assessed through 16,188 SNPs derived from the Restriction site Associated DNA Sequencing (RAD-Seq) technique. Summary statistics estimated low genetic diversity (HO&#x2009;=&#x2009;0.333-0.264) and did not reveal population differentiation within our samples (F ST&#x2009;=&#x2009;-&#xa0;0.001-0.025). Principal component analysis and a model-based clustering method did not detect a fine-scale subpopulation structure among sampling sites, however, there was genetic variability within regions and sites. Our results have revealed comparable genetic and dispersal patterns to those observed in other shallow-water snapper species in Puerto Rico waters. It is crucial to further enhance our understanding of the ecological and biological aspect of the queen snapper to effectively manage and conserve this species as fishing pressure has been extended to deep water species in the US Caribbean. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-025-00289-7.

Caribbean Fisheries↗

Genetic diversity and population structure of 20 North European cattle breeds.

Blood samples were collected from 743 animals from 15 indigenous, 2 old imported, and 3 commercial North European cattle breeds. The samples were analyzed for 11 erythrocyte antigen systems, 8 proteins, and 10 microsatellites, and used to assess inter- and intrabreed genetic variation and genetic population structures. The microsatellites BoLA-DRBP1 and CSSM66 were nonneutral markers according to the Ewens-Watterson test, suggesting some kind of selection imposed on these loci. North European cattle breeds displayed generally similar levels of multilocus heterozygosity and allelic diversity. However, allelic diversity has been reduced in several breeds, which was explained by limited effective population sizes over the course of man-directed breed development and demographic bottlenecks of indigenous breeds. A tree showing genetic relationships between breeds was constructed from a matrix of random drift-based genetic distance estimates. The breeds were classified on the basis of the tree topology into four major breed groups, defined as Northern indigenous breeds, Southern breeds, Ayrshire and Friesian breeds, and Jersey. Grouping of Nordic breeds was supported by documented breed history and geographical divisions of native breeding regions of indigenous cattle. Divergence estimates between Icelandic cattle and indigenous breeds suggested a separation time of more than 1,000 years between Icelandic cattle and Norwegian native breeds, a finding consistent with historical evidence.

Alleles↗

Sequence signatures from DNA amplification fingerprints reveal fine population structure of the dogwood pathogen Discula destructiva.

Isolates of Discula destructiva Redlin and an undescribed species of Discula, the filamentous fungi that cause anthracnose of flowering (Cornus florida L.) and Pacific (Cornus nuttalli Aud.) dogwoods, were analyzed for genetic variation by nucleic acid scanning with arbitrary mini-hairpin oligonucleotide primers. While the fungal population was highly homogeneous throughout the disease range in eastern and western North America, the generation of arbitrary signatures from amplification profiles (ASAP) distinguished isolates from the northeast, middle and southern Appalachian mountain range, and western United States and Canada. ASAP involves a dual-step arbitrary primer-based amplification procedure that generates a large number of informative allelic characters by amplification of monomorphic DNA fingerprints. ASAP analyses showed a fine fungal population structure consistent with the recent and separate introduction of the pathogen on the west and east coasts of North America.

Algorithms↗

Genetic variation and population structure of two species of neo-tropical mud-mussels (Mytella spp).

Mytella guyanensis Lamarck (1819) and Mytella charruana d'Orbigny (1846) are widespread euryhaline bivalves that have become commercially important in Brazil. Despite their importance, however, no genetic information that would be useful to orient governmental policies is available for these species. We analyzed, through allozyme electrophoresis, populations of M. guyanensis and M. charruana along 3,500 km of Brazilian coast. Pairwise comparisons among gene frequencies in M. guyanensis resulted in high levels of pairwise gene identity (I = 0.976 to 0.998). Conversely, significant levels of population structure were found in both M. guyanensis (FST = 0.089) and M. charruana (FST = 0.102). Heterozygosity levels for both species were high (H(e) = 0.090 to 0.134 in M. guyanensis and H(e) = 0.191 to 0.228 in M. charruana). The larger population size of M. charruana could explain, at least partially, the higher levels of genetic variability for this species. These levels of genetic variability yield an effective population size estimate of about 300,000 for M. guyanensis, and 540,000 for M. charruana, based on neutralist expectations. Remarkably, these numbers are much smaller than the estimated actual population sizes. This distortion might be explained by unstable population sizes and it suggests that long-term genetic variability studies are crucial to prevent artifactual viability analysis data for these commercially exploited species.

Animals↗

Diversity at the locus associated with transcription of a variable surface antigen of Pneumocystis carinii as an index of population structure and dynamics in infected rats.

Pneumocystis carinii expresses a surface glycoprotein called MSG. Different isoforms of MSG are encoded by a gene family spread over at least 15 telomeric sites. Only one locus, called UCS, supports the production of MSG mRNA. Previous studies showed that P. carinii populations from individual rats exhibited high degrees of diversity with respect to the MSG genes attached to the UCS locus. This diversity could have been generated primarily in the rats studied. Alternatively, the rats may have been infected by P. carinii organisms that were already different at the UCS locus. To investigate this issue, we examined the UCS locus in P. carinii from rats that had been exposed to few of the microbes at a specified time, which produced a bottleneck in the microbial population. Some of the rats with bottlenecks produced P. carinii populations in which a single MSG sequence resided at the UCS locus in 80 to 90% of the organisms, showing that P. carinii can proliferate within a rat without generating the very high levels of UCS diversity previously seen. From the degree of diversity observed in the bottlenecked populations, the maximum rate of switching appeared to be 0.01 event per generation. These data also suggest that the infectious dose is as low as one organism, that rats that share a cage readily infect each other, and that the doubling time of P. carinii in vivo is approximately 3 days. In addition, we found that inoculation with 10(7) P. carinii organisms from a population highly heterogeneous at the UCS locus reproduced this heterogeneity. By contrast, shifts in population structure occurred in rats given 10(4) P. carinii organisms, suggesting that a small fraction of these proliferated.

Animals↗