Showing papers in "Journal of Heredity in 1998"
TL;DR: It is demonstrated that population bottlenecks cause a characteristic mode-shift distortion in the distribution of allele frequencies at selectively neutral loci, and a qualitative graphical method is illustrated and evaluated for detecting a bottleneck-induced distortion of allele frequency distributions.
Abstract: We use population genetics theory and computer simulations to demonstrate that population bottlenecks cause a characteristic mode-shift distortion in the distribution of allele frequencies at selectively neutral loci. Bottlenecks cause alleles at low frequency ( .80) to detect an allele frequency distortion after a bottleneck of < or = 20 breeding individuals when 8 to 10 polymorphic microsatellite loci are analyzed.
1,451 citations
TL;DR: It is demonstrated that regional populations of sardines and anchovies are subject to periodic extinctions and recolonizations, and management strategies should incorporate the idea that even extremely abundant populations may be relatively fragile on ecological and evolutionary time scales.
Abstract: Most surveys of mitochondrial DNA (mtDNA) in marine fishes reveal low levels of sequence divergence between haplotypes relative to the differentiation observed between sister taxa. It is unclear whether this pattern is due to rapid lineage sorting accelerated by sweepstakes recruitment, historical bottlenecks in population size, founder events, or natural selection, any of which could retard the accumulation of deep mtDNA lineages. Recent advances in paleoclimate research prompt a reexamination of oceanographic processes as a fundamental influence on genetic diversity; evidence from ice cores and anaerobic marine sediments document strong regime shifts in the world’s oceans in concert with periodic climatic changes. These changes in sea surface temperatures, current pathways, upwelling intensities, and retention eddies are likely harbingers of severe fluctuations in population size or regional extinctions. Sardines (Sardina, Sardinops) and anchovies (Engraulis) are used to assess the consequences of such oceanographic processes on marine fish intrageneric gene genealogies. Representatives of these two groups occur in temperate boundary currents on a global scale, and these regional populations are known to fluctuate markedly. Biogeographic and genetic data indicate that Sardinops has persisted for at least 20 million years, yet the mtDNA genealogy for this group coalesces in less than half a million years and points to a recent founding of populations around the rim of the Indian–Pacific Ocean. Phylogeographic analysis of Old World anchovies reveals a Pleistocene dispersal from the Pacific to the Atlantic, almost certainly via southern Africa, followed by a very recent recolonization from Europe to southern Africa. These results demonstrate that regional populations of sardines and anchovies are subject to periodic extinctions and recolonizations. Such climate-associated dynamics may explain the low levels of nucleotide diversity and the shallow coalescence of mtDNA genealogies. If these findings apply generally to marine fishes, management strategies should incorporate the idea that even extremely abundant populations may be relatively fragile on ecological and evolutionary time scales.
1,328 citations
TL;DR: This article discusses strategies to maximize the signal:nolse ratio in genetic studies of marine species and suggests a quantitative method to correct for bias due to a common sampling problem.
Abstract: In many marine species, high levels of gene flow ensure that the genetic signal from population differentiation is weak. As a consequence, various errors associated with estimating population genetic parameters that might normally be safely Ignored assume a relatively greater importance. This fact has important implications for the use of genetic data to address two common questions in fishery conservation and management: (1) How many stocks of a given species are there? and (2) How much gene flow occurs among stocks? This article discusses strategies to maximize the signal:nolse ratio in genetic studies of marine species and suggests a quantitative method to correct for bias due to a common sampling problem. For many marine species, however, genetic methods alone cannot fully resolve these key management questions because the amount of migration necessary to eliminate most genetic evidence of stock structure (only a handful of Individuals per generation) will generally be Inconsequential as a force for rebuilding depleted populations on a time scale of interest to humans. These limitations emphasize the importance of understanding the biology and life history of the target speciesfirst, to guide design of the sampling program, and second, so that additional information can be used to supplement Indirect estimates of migration rates based on genetic data.
1,249 citations
TL;DR: Low levels of genetic dispersal between foraging specialists and a pattern of genetic differentiation consistent with matrifocal population structure and small effective population size are suggested.
Abstract: Killer whales from the coastal waters off California through Alaska were compared for genetic variation at three nuclear DNA markers and sequenced for a total of 520 bp from the mitochondrial control region. Two putative sympatric populations that range throughout this region were compared. They can be distinguished by social and foraging behavior and are known as "residents" and "transients". We found low levels of variation within populations compared to other cetacean species. Comparisons between fish (resident) versus marine mammal (transient) foraging specialists indicated highly significant genetic differentiation at both nuclear and mitochondrial loci. This differentiation is at a level consistent with intraspecific variation. A comparison between two parapatric resident populations showed a small but fixed mtDNA haplotype difference. Together these data suggest low levels of genetic dispersal between foraging specialists and a pattern of genetic differentiation consistent with matrifocal population structure and small effective population size.
279 citations
TL;DR: The hypothesis that some modern domestic sheep and European mouflon derive from a common ancestor is supported and evidence of an additional wild ancestor, other than the urial and argali groups, which has yet to be identified is provided.
Abstract: To investigate the origins and phylogenetic relationships of domestic sheep, mitochondrial DNA (mtDNA) from 243 sheep of five European, one African, and four Asian breeds and several mouflon (Ovis musimon), urial (O. vignei bochariensis), and argali (O. ammon nigrimontana, O. a. collium) were assayed for restriction fragment length polymorphisms (RFLP). Twenty haplotypes were identified which occurred in three major phlogenetic groups: urial/argali, mouflon/domestic, and domestic sheep. From the branches that contain mouflon and domestic sheep, two major domestic sheep lineages are apparent. One lineage, termed European lineage, contains the majority of haplotypes detected among European domestic sheep. These mtDNAs resemble mouflon haplotypes. The other lineage, termed Asian lineage, consists of haplotypes found in central Asian and some European domestic sheep. The mean sequence difference between these two lineages (0.72%) is of similar magnitude as that between two argali subspecies. To accurately estimate sequence differences between the European and Asian mtDNA types, the mitochondrial control region of one animal from each lineage and of one mouflon and urial were completely sequenced. Sequence comparisons show that Asian and European domestic sheep lineages differ by 4.43%. The mouflon sequences diverges from the Asian type by 4.52%, but by only 1.36% from the European type. Our data supports the hypothesis that some modern domestic sheep and European mouflon derive from a common ancestor and provide evidence of an additional wild ancestor, other than the urial and argali groups, which has yet to be identified.
241 citations
TL;DR: This study provides direct evidence for high levels of long-distance pollination in a wind-pollinated species, and contradicts traditional models of wind pollination which suggest that clouds of pollen dissipate from the source to ineffectively low densities over short distances.
Abstract: Microsatellite analysis was used to characterize pollen dispersal in a stand of 62 adult bur oaks (Quercus macrocarpa) in northern Illinois. Using PCR amplification of four dinucleotide microsatellite loci, pollen donors of 282 acorns collected from three adult trees located in different parts of the stand were determined by exclusion. Overall at least 57% of the acorns were pollinated by trees outside of the stand, because all adult trees in the stand were excluded from paternity. Average pollination distance for within-stand pollinations was 75 m, and pollen donors for two of the three maternal trees were randomly dispersed throughout the stand. These two trees also received more pollen from 50 m away than from near neighbors. Self-pollination was rare or nonexistent. This study provides direct evidence for high levels of long-distance pollination in a wind-pollinated species, and contradicts traditional models of wind pollination which suggest that clouds of pollen dissipate from the source to ineffectively low densities over short distances. Instead, the mating system of bur oak seems to be extraordinarily efficient at producing highly outbred individuals and ensuring long-range pollen flow, perhaps through pollen competition or mate choice favoring distant pollen sources.
235 citations
TL;DR: Although general patterns of genetic population structure were similar among continuously and discontinuously distributed cosmopolitan marine species, there were some striking differences, highlighting the need for a thorough understanding of the genetic basis of population structure of each species for proper management.
Abstract: Many marine fishes are cosmopolitan, occurring in continuous (e.g., circumtropical) or discontinuous (e.g., antitropical) distributions. Little is known of the genetic basis of population structure of these species, even though several support extensive fisheries. To develop a database that would facilitate comparison of the population structures among cosmopolitan fishes we consistently included restriction fragment length polymorphism (RFLP) analysis of mitochondrial DNA (mtDNA) as a common approach to our investigations of these species. This article presents a review of those analyses. Considerable intraspecific genetic variation was revealed within all cosmopolitan marine species. Continuously distributed species displayed population structures ranging from a lack of significant heterogeneity between ocean samples to shallow but significant structuring within an ocean basin. In general, greater intraspecific genetic divergence was revealed within discontinuously distributed fishes. Levels of population structuring ranged from species comprising conspecific populations with no mtDNA haplotypes in common to those comprising populations with homogeneous distributions of mtDNA haplotypes across ocean basins. The close affinity of haplotypes among conspecific populations of all discontinuously distributed species was consistent with contact since the Pleistocene. Although general patterns of genetic population structure were similar among continuously and discontinuously distributed cosmopolitan marine species, there were some striking differences. These differences underscore the need for a thorough understanding of the genetic basis of population structure of each species for proper management.
188 citations
TL;DR: It is proposed that learning could be important in the generation and maintenance of intraspecific foraging specializations and the effective conservation of genetic diversity in cetaceans with a wide distribution.
Abstract: Many cetaceans have a wide distribution in one or more oceans, and in some species, individuals migrate over an extensive range. When breeding sites are geographically distant from foraging grounds, as for a number of baleen whales, genetic stocks may be geographically isolated during a breeding season and together in a mixed assemblage during a separate feeding season. These assemblages can be spatially and temporally dynamic and pose a special problem for managers when whales are hunted on feeding grounds (as is typical). For other species seasonal migrations are less pronounced, but the same effect of locally mixing genetic stocks can develop through other mechanisms. Examples are described where intraspecific foraging specializations appear to be important in limiting gene flow between sympatric and parapatric populations. It is proposed that learning could be important in the generation and maintenance of these specializations. The effective conservation of genetic diversity in these species will require further data on both spatial and temporal components of population genetic structure.
168 citations
TL;DR: A preliminary test of the three-times rule, which depends on many assumptions about the species and genes involved, suggests that blue and fin whales should have species-specific sequences at most neutral nuclear loci, whereas humpback andfin whales should show species- specific sequences at fewer nuclear locu.
Abstract: DNA sequence analysis is a powerful tool for identifying the source of samples thought to be derived from threatened or endangered species. Analysis of mitochondrial DNA (mtDNA) from retail whale meat markets has shown consistently that the expected baleen whale in these markets, the minke whale, makes up only about half the products analyzed. The other products are either unregulated small toothed whales like dolphins or are protected baleen whales such as humpback, Bryde’s, fin, or blue whales. Independent verification of such mtDNA identifications requires analysis of nuclear genetic loci, but this is technically more difficult than standard mtDNA sequencing. In addition, evolution of species-specific sequences (i.e., fixation of sequence differences to produce reciprocally monophyletic gene trees) is slower in nuclear than in mitochondrial genes primarily because genetic drift is slower at nuclear loci. When will use of nuclear sequences allow forensic DNA identification? Comparison of neutral theories of coalescence of mitochondrial and nuclear loci suggests a simple rule of thumb. The ‘‘three-times rule’’ suggests that phylogenetic sorting at nuclear loci is likely to produce species-specific sequences when mitochondrial alleles are reciprocally monophyletic and the branches leading to the mtDNA sequences of a species are three times longer than the average difference observed within species. A preliminary test of the threetimes rule, which depends on many assumptions about the species and genes involved, suggests that blue and fin whales should have species-specific sequences at most neutral nuclear loci, whereas humpback and fin whales should show species-specific sequences at fewer nuclear loci. Partial sequences of actin introns from these species confirm the predictions of the three-times rule and show that blue and fin whales are reciprocally monophyletic at this locus. These intron sequences are thus good tools for the identification of these species and will afford a chance to identify putative hybrid blue/fin whales thought to have entered the retail market after 1989.
140 citations
TL;DR: A single molecular marker, UBC354560, is biparentally inherited, is associated with femaleness in certain genetic backgrounds, and is linked to allele A1 in the proposed two-locus epistatic genetic model of sex determination for S. viminalis.
Abstract: In many dioecious plants, gender influences economic value, breeding schemes, and/or opportunities for commercial use of genetically transformed materials. The objective of this study was to identify molecular markers linked to sex determination loci in the dioecious plant Salix viminalis L. A 4 3 4 factorial mating design was used to identify sex ratios in full-sibling progeny, to generate a working genetics model for segregating sex ratios, and to search for molecular markers linked to sex determination genes. Bulked segregant analysis, utilizing 380 arbitrary decamer primers to generate randomly amplified polymorphic DNA (RAPD) products was initially applied to progeny sets from 3 of the 16 full-sibling families. Of the 1080 RAPD bands examined, only a single 560 bp band was shown to be linked to a sex determination locus. The same 560 bp band occurred in three additional fullsibling families and was present in one female parent and one male parent involved in the factorial mating design. This marker, UBC354560, is biparentally inherited, is associated with femaleness in certain genetic backgrounds, and is linked to allele A1 in the proposed two-locus epistatic genetic model of sex determination for S. viminalis. Southern blots confirmed marker homology among progeny and parents used in this study.
126 citations
TL;DR: The studies compiled in this volume highlight the scope and imaginative uses of genetic information for conservation challenges in the marine realm.
Abstract: Author(s): Avise, JC | Abstract: Techniques for DNA and protein assay make possible genetic studies on any species. In recent years, molecular methods have been applied to a number of conservation-relevant genetic issues for marine organisms ranging from zooplankton to whales. To introduce these symposium proceedings, I will mention some of the unusual challenges and opportunities afforded by marine taxa for genetic research in conservation. Marine organisms often are less accessible for behavioral and natural history observation than are their terrestrial counterparts. Many marine organisms have exceptional dispersal and migratory capabilities. Species' ranges can be vast. Life histories may include high fecundities and explosive reproductive potentials. Many marine species of conservation concern are harvested commercially or illegally and thus economic, social, jurisdictional, and forensic matters often arise in population management, in addition to biological considerations. For a diversity of marine taxa, molecular markers have uncovered previously unknown aspects of behavior, natural history, and population demography that can inform conservation and management decisions. The studies compiled in this volume highlight the scope and imaginative uses of genetic information for conservation challenges in the marine realm.
TL;DR: Genotypes at the allozyme locus thus appear to vary in part as a function of the sex and age composition of samples, serving as a warning that genetic markers may not necessarily be independent with respect to life-history parameters such assex and age.
Abstract: We examined variation in mitochondrial DNA (mtDNA) among geographic samples of seven species of marine fish sampled from the Gulf of Mexico (Gulf) and along the southeastern Atlantic coast of the United States (western Atlantic). Species included three sciaenids that are estuarine dependent during larval and juvenile stages, three reef-associated species that are typically found as adults on reefs, hard bottoms, or submerged structures, and one scombrid that is pelagic throughout its life history. All seven species are significant components of recreational and/or commercial fisheries, and the issue of population structure/gene flow is critical to their conservation and management. MtDNA variation in the three sciaenids is consistent with the hypothesis that dispersal/gene flow in all three species follows an isolation-by-distance model, and that dispersal potential is consistent with expectations based on life history. No evidence of population structuring was observed in the three reef-associated species, in contrast to what might be expected on the basis of their adult life history. Low levels of mtDNA variation in two of the reef-associated species is consistent with the occurrence of past or presentday bottleneck events. MtDNA variation in the scombrid was not structured geographically, consistent with expectations for a highly pelagic species, but was discordant with variation observed at an allozyme locus (PEPA-2). However, variation in mtDNA was independent of sex or age of individuals, whereas variation at the allozyme locus was not. Genotypes at the allozyme locus thus appear to vary in part as a function of the sex and age composition of samples. This finding serves as a warning that genetic markers may not necessarily be independent with respect to life-history parameters such as sex and age.
TL;DR: Evidence for selective maintenance of genetic diversity at the major histocompatibility complex (MHC) was investigated in an unmanaged population of Soay sheep on the island of Hirta, St. Kilda, Scotland, indicating the action of balancing selection favoring novel MHC variants and hence increased diversity over a longer time period.
Abstract: Evidence for selective maintenance of genetic diversity at the major histocompatibility complex (MHC) was investigated in an unmanaged population of Soay sheep on the island of Hirta, St. Kilda, Scotland. Animals were sampled as newborn lambs and between 887 and 1209 individuals were typed at each of five microsatellite markers located either within or flanking the ovine MHC. Markers located within the MHC showed high levels of linkage disequilibrium with each other but not with flanking markers. Hardy-Weinberg proportions were found for all loci; however, two of the three markers within the MHC showed relatively even allele frequency distributions that were unlikely to have resulted from neutrality and suggest the action of recent balancing selection. Sequence polymorphism was examined within DRB, a class II gene immediately adjacent to one of the microsatellite markers, and high correlation of sequence polymorphism with microsatellite length variation was found. An excess of nonsynonymous substitution compared to synonymous substitution was found, indicating the action of balancing selection favoring novel MHC variants and hence increased diversity over a longer time period.
TL;DR: It is hypothesize that the cause of both low levels of molecular diversity and small effective population sizes of the two species is the impact of glaciation during the past 20,000 years.
Abstract: Molecular population genetic diversity of two planktonic copepods of the North Atlantic, Calanus finmarchicus and Nannocalanus minor (Crustacea, Copepoda, Calanoida), was characterized using the sequence variation in a 350 bp region of the mitochondrial 16S rRNA gene. The subarctic species, C. finmarchicus, shows lower population genetic diversity (haplotype diversity, h = 0.368, SD = 0.043; nucleotide diversity, pi = 0.00370, SD = 0.0026) than the temperate/subtropical species, N. minor (h = 0.824, SD = 0.024; pi = 0.00502, SD = 0.0032). Effective population sizes (N(e), estimated from numbers of haplotypes) and effective female population sizes (Nf(e), estimated from nucleotide diversities) for the two species are 10(7) to 10(10) smaller than census female population sizes (Nf) estimated from observed densities and areal distributions. For both C. finmarchicus and N. minor, Nf approximately 10(15), N(e) approximately 10(8), and Nf(e) approximately 10(5). We hypothesize that the cause of both low levels of molecular diversity and small effective population sizes of the two species is the impact of glaciation during the past 20,000 years. C. finmarchicus may have experienced 75% range reduction and latitudinal displacement during the last glacial maximum at 18,000 years BP, giving rise to a genetic bottleneck; this may explain low diversity and an L-shaped distribution of pairwise haplotype differences. In contrast, N. minor may have experienced range reduction of only 30% and less change in latitudinal extent, with less impact of levels of molecular diversity and the shape of the pairwise difference distribution. Although marine zooplankton species are highly abundant, conservation biologists should note that their numbers may vary significantly on climatic to evolutionary time scales, generating low levels of molecular genetic diversity.
TL;DR: By constraining genetic differentiation among populations, amphidromy may impede speciation in these fishes, possibly explaining why the Hawaiian freshwater fish fauna is depauperate compared to other species-rich Hawaiian faunas.
Abstract: MtDNA sequencing was used to assess the phylogeographic structure of four species of Hawaiian freshwater fishes: Lentipes concolor, Stenogobius hawaiiensis, Sicyopterus stimpsoni, and Awaous guamensis. Samples of each species were collected from streams on the northeast side of Kauai, Maui, Molokai, Oahu, and Hawaii. We sequenced segments from both coding and noncoding regions (638-1391 bp) in each species. Sequence analysis uncovered genetic variability in these fishes but no evidence of strong geographic structure among island populations. This result is most readily explained by the fishes' larval marine life stage (amphidromy), which likely facilitates gene flow among island populations. By constraining genetic differentiation among populations, amphidromy may impede speciation in these fishes, possibly explaining why the Hawaiian freshwater fish fauna is depauperate compared to other species-rich Hawaiian faunas. It may also provide them with a kind of evolutionary flexibility atypical of other, more isolated island faunas and allow natural restocking to occur in streams that have been restored to suitable conditions. Comparisons of restriction site and sequence data suggested similar population genetic conclusions for all species except S. stimpsoni, for which the restriction site data is questioned.
TL;DR: The UPGMA phylogenetic tree, derived from Nei's genetic distances, shows the presence of intraspecific differentiative processes affecting mainly the two island populations, Réunion and Hawaii.
Abstract: Multilocus enzyme electrophoresis data from 26 polymorphic loci (124 alleles) were used to analyze the genetic aspects of the worldwide colonization of Ceratitis capitata (medfly). Eighty-two samples of 17 populations were collected from six regions throughout the species range: Africa, extra-Mediterranean islands (Madeira and Gran Canaria), Mediterranean region, Latin America (Guatemala), Pacific (Hawaii), and Australia. The variability parameters (H, P, A) reveal that the geographical dispersal of medfly from its ancestral source area (East Africa) is associated with a great reduction in variability. The pattern of decreasing variability occurs at two regional levels: in the African-Mediterranean region where the differentiation is gradual, and in the Latin American-Pacific region where some ancestral variability is still present as a consequence of recent colonization. The UPGMA phylogenetic tree, derived from Nei's genetic distances, shows the presence of intraspecific differentiative processes affecting mainly the two island populations, Reunion and Hawaii. The population genetic changes observed in the species range are consistent with both the chronology and the historical circuitous course of the medfly colonization process.
TL;DR: Results suggest that the original null allele (as well as the nonnull class), which was cloned and characterized from the White Sands pupfish, has diversified considerably since its origin and has not recombined frequently with the non null class of alleles.
Abstract: Author(s): Jones, AG; Stockwell, CA; Walker, D; Avise, JC | Abstract: Microsatellite loci were cloned and characterized from the White Sands pupfish (Cyprinodon tularosa), a New Mexico state-listed endangered species. One locus exhibited a high-frequency nonamplifying allele localized to a single population. This null allele was PCR amplified by redesign of one of the original primers and multiple individuals homozygous for null as well as for nonnull alleles were sequenced using the new primer. These molecular dissections revealed that the original failure to amplify some alleles from this microsatellite locus was due to a 4 bp deletion in one of the original PCR priming sites. Furthermore, the reamplifications revealed five distinct size classes of alleles that had been masquerading as the original null. These null alleles did not overlap in length with the nonnull alleles, and they also differed consistently by a linked nucleotide substitution. Results suggest that the original null allele (as well as the nonnull class) has diversified considerably since its origin and has not recombined frequently with the nonnull class of alleles.
TL;DR: The rDNA localization indicated that chromosome rearrangements as centric shifts, centric fusions, and translocations of NORs involve in a decrease of rDNA loci number during the evolution of the complex of Hypochaeris species probably from an ancestral genome.
Abstract: The pattern of rDNA sequence distribution in 11 Hypochaeris species from South America and Europe has been determined by in situ hybridization using probes of 18S-5.8S-28S and 5S ribosomal RNA genes. Activity of nucleolar organizer regions (NORs) was tested by silver nitrate staining and chromomycin A3 banding of European species was carried out. In European species the 18S-5.8S-28S rRNA genes were located in the terminal secondary constrictions and the adjacent satellites, except for one locus in H. achyrophorus. In South American species, one or two 18S-5.8S-28S rDNA loci were observed in the intercalary secondary constrictions. All the rDNA sites appeared active, except one locus in H. chillensis. With the exception of H. cretensis, 5S rRNA genes were located on a single chromosome pair. In all the species analyzed, GC-rich heterochromatin has been located around the NORs. The rDNA localization indicated that chromosome rearrangements as centric shifts, centric fusions, and translocations of NORs involve in a decrease of rDNA loci number during the evolution of the complex of Hypochaeris species probably from an ancestral genome with two loci of 18S-5.8S-28S rDNA and one locus of 5S rDNA.
TL;DR: The results suggest that microsatellite DNA markers are a useful tool for studying the genetic relationships among chicken breeds.
Abstract: Genetic relationships among Japanese native breeds of chickens were studied on the basis of microsatellite DNA polymorphisms. DNA samples from 10 Japanese native breeds (Iwate-Jidori, Aizu-Jidori, Sadohige-Jidori, Siba-Tori, Onaga-Dori, Echigonankin, Hinai, Kinpa, Koeyoshi, and Tomaru) and one imported breed (White Leghorn) were analyzed using eight microsatellite markers that were isolated from a microsatellite DNA-enriched library of chickens (Takahashi et al. 1996). The PCR primers to detect (CA)n repeat length polymorphisms were synthesized based on the sequences of clones, and these markers were typed by PCR amplification and electrophoresis using a DNA sequencer. Since all eight microsatellite markers were polymorphic, genetic distance between the breeds could be calculated based on the frequencies of alleles of the microsatellites and phylogenetic relationships between the breeds could be estimated. Most Japanese native chickens were grouped into three groups that correspond to the origin breeds, Jidori, Shokoku, and Shamo. The results suggest that microsatellite DNA markers are a useful tool for studying the genetic relationships among chicken breeds.
TL;DR: A generic analysis is presented that relates gene pool separation to the ability to assign individuals, an analysis that does not depend on the type of marker, and strengths and weaknesses of different DNA markers are reviewed.
Abstract: An emerging problem of some interest is whether we can determine the population membership of a single individual, using a population-specific "genetic fingerprint." The levels of accuracy and precision required are beyond the reach of allozyme analysis, and attention has shifted to DNA polymorphisms. There are different types of DNA markers available for population surveys: RFLPs, mini- and micro-satellites, and RAPDs, and each type has its own strengths and weaknesses. We present a generic analysis that relates gene pool separation to our ability to assign individuals, an analysis that does not depend on the type of marker. We then review strengths and weaknesses of different DNA markers, in the context of DNA fingerprinting. Codominant loci are best. It is possible to gain more information per marker with multiallelic loci, but diminishing returns set in rapidly, and it is better to add loci. A modest number of independent loci is best, each locus with a modest number of alleles and with each allele in modest frequency.
TL;DR: It is suggested that the Andean mountain cat diverged from a common ancestor with the ocelot (Leopardus paradalis) and margay and exhibits moderate levels of genetic variation.
Abstract: Rarely observed in the wild, the existence of the Andean mountain cat (Oreailurus jacobita) has been established based on only 3 skulls and 14 museum skins The Andean mountain cat's evolutionary relationship to other felids based on morphological characters is largely contradictory, with evidence aligning it with South American small spotted cats (ocelot lineage) or alternatively with pantherine lineage felids Here we describe the phylogenetic distinctiveness and placement of the Andean mountain cat using DNA extracted from pieces of nine independent pelt specimens, including one confiscated from a trapper in 1995 A phylogenetic analysis of DNA sequences from three rapidly evolving mitochondrial genes (16S rRNA, NADH-5, and ATP-8) indicate that the Andean mountain cat is a distinct species belonging to the ocelot lineage Our findings suggest that the Andean mountain cat diverged from a common ancestor with the ocelot (Leopardus paradalis) and margay (L wiedii) and exhibits moderate levels of genetic variation
TL;DR: All three types of gametogenesis are confirmed by mating two females of P. eos-neogaeus to a male of a related species, P. oreas, whose distinctive contribution to the offspring was revealed through morphology, genome size, and tissue graft analysis.
Abstract: We have previously reported that the all-female species Phoxinus eos-neogaeus is perpetuated at Norton Pool, New Hampshire, by clonal reproduction. Genetically identical diploid eos-neogaeus ova develop into diploid offspring if congeneric sperm stimulates development, and into triploid or diploid-triploid mosaic offspring if syngamy occurs. Some individuals produce both genetically identical and unique diploid ova, resulting in clonal and nonclonal offspring. In a third, very different type of gametogenesis, other females produce haploid eos ova that yield diploid ‘‘P. eos’’ offspring if fertilized by P. eos sperm. In this study we confirmed all three types of gametogenesis by mating two females of P. eos-neogaeus to a male of a related species, P. oreas, whose distinctive contribution to the offspring was revealed through morphology, genome size, and tissue graft analysis. In a second set of experiments we show that the same clone has existed at Norton Pool for 11 years. Lastly, we show that gynogenetic reproduction is not restricted to Norton Pool, but that hybrids from Algonquin Park, Ontario, also reproduce clonally.
TL;DR: A cluster analysis of genetic similarities among cultivars revealed three major clusters that correspond to the three major racial groupings of cultivated avocado.
Abstract: Anonymous DNA fragments from the genome of cultivated avocado (Persea americana Mill.) were cloned into a plasmid vector and used to screen a total of 36 cultivars. There is a high level of polymorphism among cultivars allowing all cultivars to be assigned a unique genotype based on 14 genetic loci. A cluster analysis of genetic similarities among cultivars revealed three major clusters that correspond to the three major racial groupings of cultivated avocado. Additional clusters appear to reflect cultivars derived through interracial hybridization.
TL;DR: Joint analysis of the allozyme and mtDNA data indicates that introgression may be occurring between all three species in Puget Sound and that it may be an important source of diversity in Sebastes.
Abstract: The genus Sebastes comprises at least 100 species worldwide and is the largest genus of marine fishes in the eastern North Pacific. Species within the genus are closely related, and many sibling species exist. Allozyme analysis and restriction analyses of mitochondrial DNA (mtDNA) were used to investigate genetic differentiation and introgression within and among three nearshore species of the subgenus Pteropodus, Sebastes auriculatus (brown rockfish), S. caurinus (copper rockfish), and S. maliger (quillback rockfish). Geographic differentiation was detected within each species in collections ranging from California to southeast Alaska. In addition, significant shifts in allozyme frequencies were noted for S. maliger from Puget Sound, Washington, and adjacent areas separated by less than 70 km. Alleles characteristic of the other two species were absent from samples of S. maliger outside Puget Sound but were consistently observed within Puget Sound. Joint analysis of the allozyme and mtDNA data indicates that introgression may be occurring between all three species in Puget Sound and that it may be an important source of diversity in Sebastes.
TL;DR: In this article, the authors present linkage maps and estimate genome length for two hybrid individuals of Douglas-fir [Pseudotsuga menziesii (Mirb.) Franco], a coniferous tree species of wide distribution in the western United States.
Abstract: We present linkage maps and estimate genome length for two hybrid individuals of Douglas-fir [Pseudotsuga menziesii (Mirb.) Franco], a coniferous tree species of wide distribution in the western United States. The hybrids were produced by crosses between the coastal (var. menziesi~) and interior (var. glauca) varieties. Haploid megagametophytes from 80 seeds of each individual were analyzed using 81 10-by random amplified polymorphic DNA (RAPD) primers selected for polymorphism, fragment strength, and repeatability in preliminary segregation analysis. Most (82-90%) of the segregating fragments followed the expected 1:1 Mendelian segregation; however, 10-18% showed significant segregation distortion (P < .05) among megagametophytes of the two trees. In one tree, 201 of 221 segregating loci analyzed were combined into 16 major linkage groups of 4 or more loci (plus 1 group of 3 loci, 3 groups with pairs of loci, and 11 unlinked loci); in the other, 238 of 250 segregating loci were combined into 18 major groups (plus 2 groups of 3 loci each and 6 unlinked loci). Analyses of the distribution of markers indicated highly significant clustering in both trees (P < .001). Including flanking regions and unlinked loci, both trees had linkage maps of similar length, 2600 cM and 3000 cM; expected total map size ranged from 2800 to 3500 cM based on method-of-moments estimation. When a common RAPD protocol was used, more than one-third of the RAPD markers segregated in both hybrids. These maps of Douglas-fir are among the largest reported for conifers, a possible consequence of its 13 haploid chromosomes.
TL;DR: Epistasis is involved in the genes for major flesh colors in watermelon, with ii inhibitory to CC (canary yellow), resulting in red flesh, and CC (in the absence of ii) epistatic to YY, producing canary flesh.
Abstract: Watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai] flesh color is controlled by several genes to produce red, orange, salmon yellow, canary yellow, or white. The objective of these experiments was to study the interaction of three independently reported gene loci, each having two or three alleles: C (canary yellow) versus c (red), y (salmon yellow) versus Y (red) versus y8 (orange), and i (inhibitory to C) versus I (noninhibitory to C). The interaction of C, y, y8, and i is of interest to those developing new cultivars of watermelon and has not been reported previously. Five crosses were used to study gene action: Yellow Baby 3 Tendersweet Orange Flesh, Yellow Doll 3 Tendersweet Orange Flesh, Yellow Baby 3 Golden Honey, Yellow Doll 3 Golden Honey, and Yellow Baby 3 Sweet Princess. Based on performance of PA, PB, F1, F2, BC1A, and BC1B, the parents have the following genotypes: Yellow Baby 5 CCYYII, Yellow Doll 5 CCYYII, Tendersweet Orange Flesh 5 ccy8y8II, Golden Honey 5 ccyyII, and Sweet Princess 5 ccYYii. Segregation of flesh color in the progeny of the five families supported the previous report of a multiple allelic series at the y locus, where Y (red) was dominant to y8 (orange) and y (salmon yellow). In conclusion, epistasis is involved in the genes for major flesh colors in watermelon, with ii inhibitory to CC (canary yellow), resulting in red flesh, and CC (in the absence of ii) epistatic to YY, producing canary flesh.
TL;DR: Analysis of Mendelian crosses between strains of L. boulardi of opposite immune suppressive abilities indicated that the trait is controlled by a single chromosomal factor with semidominant effect, demonstrating that the gene-for-gene model commonly found in plant-parasite interactions may also explain natural variations in insect-parasant traits.
Abstract: Encapsulation has evolved as an efficient mechanism whereby an insect host can survive infection by parasitoids This ability is controlled by a major gene in Drosophila melanogaster hosts. The parasitoid Leptopilina boulardi (Hymenoptera Eucoilidae) can suppress the Drosophila immune reaction by injecting viruslike particles. Analysis of Mendelian crosses between strains of L. boulardi of opposite immune suppressive abilities indicated that the trait is controlled by a single chromosomal factor with semidominant effect. We developed a method to test the monogenic hypothesis. The range of possible genotypic values in back-crosses was studied using various progeny that were genotypically homogenous. These could be obtained because of the arrhenotokous mode of reproduction. The progeny groups were divided into two clusters according to the major gene classification and the hypothesis of another unlinked genetic factor was rejected. Lastly, there was a residual progeny effect within the major groups, indicating that minor genes are also present. This study rules out the polygenic effect for a trait governing the interaction between the insect and parasitoid. It demonstrates that the gene-for-gene model commonly found in plant-parasite interactions may also explain natural variations in insect-parasitoid traits.