No full-text available
To read the full-text of this research,
you can request a copy directly from the authors.
REAP: An Integrated Environment for the Manipulation and Phylogenetic Analysis of Restriction Data
... 22). Estos análisis se realizaron con el programa REAP 4.0 (McElroy et al. 1992). Se realizó una prueba exacta de homogeneidad en la distribución de haplotipos para la cual se estimó la significancia estadística mediante simulaciones Monte Carlo de acuerdo con Raymond y Rousset (1995). ...
... 22). These analyses were made using the program REAP 4.0 (McElroy et al. 1992). We applied an exact test of haplotype homogeneity among samples and the statistical significance was estimated via 1000 Markov Chain Monte Carlo simulations as proposed by Raymond and Rousset (1995). ...
Patterns of genetic structure among marine populations involve a variety of dispersal mechanisms and spatial scales. Pelagic species, such as the dolphinfish Coryphaena hippurus, epitomize the open and continuous nature of the marine environment due to their extensive migrations. Many studies have revealed that oceanic pelagic species tend to be genetically homogeneous over local and often extended geographic scales and only show levels of differentiation among extreme localities or ocean basins. Here we present genetic data suggesting genetic heterogeneity in the dolphinfish at geographic scales much smaller than those predicted by those generalizations. Mitochondrial NADH1 gene RFLPs revealed a highly significant (ΦST = 0.029, P = 0.004, AMOVA) molecular genetic structure among fish from Baja California Sur (BCS), Sinaloa and Hawaii, consistent with heterogeneous haplotype frequencies (P = 0.014, exact test of genetic differentiation) and a depressed molecular diversity in fish sampled off BCS.
... Each fish was then characterized by an eight-letter composite haplotype code; each letter representing the restriction site code for each of the eight enzymes (e.g., AAAAAAAA, ABAAAAAA). A site matrix for each of the composite haplotypes resolved was constructed using the program REAP (McElroy et al. 1992). The composite haplotype restriction site matrix so generated formed the basis for subsequent analyses of haplotype and nucleotide diversity within populations and nucleotide divergence (Nei and Tajima 1981) among populations using programs in TABLE 1. Presence (1) and absence (0) restriction site matrix for threespine stickleback mitochondrial DNA haplotypes resolved with eight restriction enzymes. ...
... These lakes represent one of the lake-stream pairs on Graham Island (Drizzle) and a population apparently fixed for the Marine lineage (Rouge Lake), respectively (Reimchen et al. 1985;O'Reilly et al. 1993;Deagle et al. 1996). Frequency distributions of mtDNA haplotypes among populations were compared using chi-square randomization tests using MONTE of REAP (McElroy et al. 1992). All statistical tests involving multiple simultaneous tests were considered significant at a "tablewide" a-level of 5% using the sequential Bonferroni procedure (Rice 1989). ...
Three drainage systems in British Columbia, Canada, contain divergent parapatric lake-stream pairs of threespine sticklebacks (Gasterosteus aculeatus): Drizzle and Mayer Lakes on Graham Island, Queen Charlotte Islands, and Misty Lake on northeastern Vancouver Island. Ecological and morphological differences between members of all three lake-stream pairs are strikingly similar; lake fish are melanistic and slim bodied with smaller mouths and more gill rakers than the mottled-brown and robust-bodied stream sticklebacks. We estimated the level of genetic divergence between lake and stream fish in Misty Lake and tested hypotheses of single versus multiple origins of the pairs by assaying mitochondrial DNA (mtDNA) restriction site variation in samples from the three lake systems. MtDNA analysis revealed the existence of two highly divergent lineages differing by 2.7% in sequence. One lineage predominated in Misty stream fish (73%), whereas the other lineage predominated in Misty Lake samples (96%). Comparable forms (lake or stream) in the different lakes did not cluster together in terms of mtDNA nucleotide divergence, suggesting that the pairs have had independent origins. We concluded that: (1) divergent mtDNA lineages in North Pacific sticklebacks stem from historical isolation in the two major glacial refugia proposed for the North Pacific (Beringia and Cascadia); (2) the stream and lake pair in Misty Lake are distinct gene pools; (3) the divergence between parapatric lake and stream Gasterosteus represents parallel evolution having occurred at least twice in the North Pacific; and (4) different scales of evolutionary divergence exist in North Pacific Gasterosteus, that is, a relatively ancient divergence of mtDNA clades as well as recent (i.e., postglacial) divergence of ecotypes within major clades.
... Because small mtDNA fragments less than 400 base pairs could not been scored, estimates of nucleotide sequence divergence (p) among mtDNA haplotypes were calculated by the method of Nei & Li (1979) from the total proportion of shared mtDNA fragments between two individuals. Measures of diversity within populations were estimated using the DA DA program in the REAP REAP 4.0 package (McElroy et al., 1992). Genetic heterogeneity within populations was estimated by haplotype diversity (h) and nucleotide diversity (p) within populations, and nucleotide divergence (dxy) among populations (Nei & Tajima, 1981). ...
... The degree of geographical heterogeneity of mtDNA haplotype distributions was assessed using a (v 2 ) statistic as described by Ro & Bentzen (1989). The signi®cance level was obtained by 10 000 Monte Carlo randomizations using the MONTE MONTE program from the REAP REAP 4.0 package (McElroy et al., 1992). ...
... The degree of nucleotide divergence was estimated using the REAP computer package (McElroy et al., 1992). Neighbour-Joining method (Saitou and Nei, 1987) was used for the construction of the phylogenetic trees. ...
... The degree of geographical heterogeneity of mtDNA haplotype distribution was assessed using X 2 statistics as described by Roff and Bentzen (1989). For restriction site data, Monte-Carlo randomization tests were performed to determine the significance of haplotype frequency distributions among sampling sites using MONTE program from REAP package (McElroy et al.,1992). ...
The phylogenetic relationship among five shad species (Alosa caspia, A. fallax nilotica, Alosa maeotica, Alosa
immaculata, Alosa tanaica) from Turkish marine waters was investigated with mitochondrial DNA polymerase chain reaction-restriction fragment length polymorphism.The six genesegments, NADH 5/6, NADH 3/4cytochrome b, COX, 16 SrRNA and D-Loop,of mtDNA amplified by PCR were digested with seven restriction enzymes, BsurI, AluI, EheI, Hin6I, RsaI, XhoI Bsh1236I,respectively.When all the six genes were combined together for phylogenetic analysis, a total of 45 haplotypes were detected from the five shad species, and the average haplotype diversity and nucleotide diversity within species were 0.8809 and 0.0022 respectively. The average nucleotide diversity and nucleotide divergence among species were 0.009248 and 0.007080 respectively. The highest genetic divergence was observed between A. caspiaand A. maeotica
(0.013727) and the lowest between A. immaculataand A. tanaica (0.003073). Monte Carlo (X2) pairwise genetic comparison revealed highly significant differences between all species (P<0.001). In the Neighbour-joining tree, there were two main grouping, and in the first group, A. caspia and A. f. nilotica exhibited the closest genetic similarity which was the sister group to A. immaculata. A .tanaicaseems to be the most divergent in this grouping. Another group contained only A. maeotica which
showed the highest genetic differentiation among Alosa genus.
... Population pairwise differentiation tests also were conducted using Arlequin 1.1. Because so many singlets (haplotypes unique to one individual) were found in our data set, we also used a randomized Chi-square test of independence using the Monte Carlo method in REAP to test for heterogeneity between haplotype frequencies (McElroy et al. 1992). Ten thousand simulations were compared to the original matrix to minimize the effect of small sample size caused by singlets (Roff and Bentzen 1989). ...
White-winged Doves (Zenaida asiatica) in Texas are separated into four subspecies primarily based on morphological variation. However, problems differentiating the subspecies by morphological measurements alone and a recent range expansion have led to questions about their systematic status and population structure. We evaluated both morphological characters and a 289 base-pair segment of the mitochondrial control region from 183 White-winged Doves taken from 31 locations in Texas, New Mexico, and Arizona. Twenty-seven variable base changes were observed, which resulted in 44 haplotypes. An analysis of haplotypes yielded little phylogenetic signal; however, analyses of haplotype frequencies indicated geographic heterogeneity between doves collected in the four historic subspecies ranges. Doves from the range expansion areas were intermediate in size and genetically homogenous. Morphological analyses suggested congruency between control region variation and body size. Our data support the recognition of two subspecies of White-winged Doves with a zone of intergradation in the range expansion areas. The dispersal of White-winged Doves into the expansion areas appears to be a congruent process by both subspecies.
... Composite haplotypes (hereinafter haplotypes) were constructed from restriction fragment patterns of all 12 restriction enzymes across the combined PCR amplified A8/A6/COIII/ND3/ND4L/ND4 region. For each of the composite haplotypes resolved, a binary character state matrix was produced using the REAP software package (McElroy et al. 1992). ...
The Pacific smelt Osmerus dentex is widely distributed in the North Pacific and Arctic seas and belongs to the species that may shed light on the biogeography and evolutionary history of Arctic marine fauna. O. dentex came into existence in the northwestern Pacific at the Pliocene–Pleistocene border and could widely spread along the Eurasian and North American coasts. We assessed the impact of global climatic and geological changes on the formation of the genetic structure of O. dentex in the Eurasian parts of the species area using a variety of phylogenetic methods and molecular dating. The results were interpreted in conjunction with paleoclimatic evidence. Phylogeographic patterns based on cytb and coI sequences, and RFLP ND3/ND4L/ND4 and A8/A6/COIII/ND3 mtDNA regions for 462 Pacific smelts from 25 Eurasian locations were analyzed. Our results suggest that (1) geographical distribution observed for mtDNA haplotypes resulted from influences of historical range expansions, episodes of long-distance colonization and restricted dispersal; (2) the main refugium was located in the northwestern Pacific and the genetic similarities observed among and within geographical regions probably originated from postglacial recolonization from common sources; (3) an additional small refugium in the White Sea existed in the Late Pleistocene.
... Statistical significance of the hierarchical components of variance and the corresponding F statistics was estimated from the nonparametric distribution of the pseudo-probability test [21]. The divergence estimates [23,24] between sympatric and allopatric charr populations, including additional samples of S. m. malma across the range [16], were calculated in the REAP software package [25]. Historical demographic processes were tested by the distribution of nucleotide substitutions between all pairs of haplotypes (mismatch distribution) [26,27] in the Arlequin vers. ...
The present-day contact zone between the Beringian and Arctic phylogenetic lineages of charrs of the genus Salvelinus in the Northwest Pacific is documented. A comparative analysis of the genetic differentiation and divergence indices for allopatric and sympatric populations of charrs and phylogenetic and genealogical analyses of the mtDNA haplotypes indicate that Lake Achchen and the Lake Pekulineiskoe are the zones of secondary contact between S. m. malma and S. taranetzi; Lake Nachikinskoe, between S. m. malma and Salvelinus sp. 4; and Lake Dal’nee, between S. m. malma and S. krogiusae. The level of divergence between phylogenetic groups of haplotypes considerably exceeds the range of intraspecific variability of S. m. malma and could not have been achieved after colonization of the lakes in conditions of sympathy. The obtained data suggest that the territory of Kamchatka was colonized by the common ancestor of the Arctic phylogroup of Taranetz charr.
... Estimates of nucleotide divergence and dendrogram topology were made using the PAUP version 4.0b10 software package [45]. The main genetic variation indices were estimated using the REAP [46] and ARLEQUIN version 2.0 [28] software packages. Heterogeneity of haplotype frequencies between each sample pair was evaluated using the Monte Carlo method (1000 pseudorandom replicates [47]). ...
The genetic variation and population structure of narrow-clawed crayfish (Astacus leptodactylus) was examined by means of polymerase chain reaction (PC R) restriction fragment length polymorphism (RF LP) analysis of the cytochrome oxidase subunit I (COI) of mitochondrial DNA. A total of 194 adult specimens were collected from seven sample sites including, two in the south Caspian Sea and one each in Anzali wetland and Aras reservoir and three rivers Chafrood, Masule Rudkhan and S iah Darvishan. The PCR products were digested with 19 restriction enzymes and five enzymes revealed polymorphism patterns (DdeІ, MboІ, TaqI, RsaІ and HinfІ). Twenty eight composite haplotypes were showed with the number of haplotypes in each population sample ranging from 8 to 13. Private haplotypes were found at very low frequencies. Two regional (S iah Darvishan River and Astara) groups were clearly recognized by cluster and molecular variance model (AMOVA) analyses (P<0.0001). Each of these groups revealed dominant haplotypes while these haplotypes play less important rule in population structures of the other geographic areas. Intrapop ulatio n hap lo type (h) and nucleotide (π) diversities were high for each locality, ranging h=0.7560±0.030 and π=0.00334±0.00301, respectively. Results of this study discerned two divergent populations of narrow-clawed crayfish including S iah Darvishan River and Astara. Thus, the population structure of the narrow-clawed crayfish, as inferred from mtDN A analysis, is constituted by genetica lly separate groups that nearly reflect their geographic distribution.
... provide not just an exact test of the overall homogeneity in n x T matrices, as do other programs like CHIRXC (ftp://statgen.ncsu.edu/pub/zaykin/) [Zaykin and Pudovkin, 1993] and REAP [McElroy et al., 1992], but also the exact tests for the pairwise comparison between spectra as well. A COLLAPSE program [Khromov-Borisov et al., 1999] (nikita@dna.cbiot.ufrgs.br, ...
The study and comparison of mutation(al) spectra is an important problem in molecular biology, because these spectra often reflect on important features of mutations and their fixation. Such features include the interaction of DNA with various mutagens, the function of repair/replication enzymes, and properties of target proteins. It is known that mutability varies significantly along nucleotide sequences, such that mutations often concentrate at certain positions, called “hotspots,” in a sequence. In this paper, we discuss in detail two approaches for mutation spectra analysis: the comparison of mutation spectra with a HG-PUBL program, (FTP: sunsite.unc.edu/pub/academic/biology/dna-mutations/hyperg) and hotspot prediction with the CLUSTERM program (www.itba.mi.cnr.it/webmutation; ftp.bionet.nsc.ru/pub/biology/dbms/clusterm.zip). Several other approaches for mutational spectra analysis, such as the analysis of a target protein structure, hotspot context revealing, multiple spectra comparisons, as well as a number of mutation databases are briefly described. Mutation spectra in the lacI gene of E. coli and the human p53 gene are used for illustration of various difficulties of such analysis. Hum Mutat 17:83–102, 2001. © 2001 Wiley-Liss, Inc.
... The genetic differentiation of whitefish ecotypes within each lake was evaluated from the analysis of frequency distribution of each individual genotype and of mtDNA phylogenetic groups using X 2 randomization tests (Roff and Bentzen 1989) with 1000 randomizations using the MONTE program of the REAP software package (McElroy et al. 1992). The extent of gene flow between pairs of ecotypic forms was evaluated from F st estimates (Wright 1978) by considering the mitochondrial genome as a unique locus with mtDNA genotypes corresponding to distinct alleles (Chapman 1989). ...
We assessed variation in mitochondrial DNA (mtDNA) by restriction fragment length polymorphism (RFLP) analysis and in nuclear genes by allozyme analysis among sympatric pairs of limnetic and benthic ecotypes of whitefish (Coregonus) coexisting in three lakes of southern Yukon to address three evolutionary questions regarding their origins. Are sympatric low and high gill-raker count ecotypes genetically differentiated? Are they issued from monophyletic or polyphyletic evolutionary events? If they are polyphyletic in origins, did they originate from multiple allopatric speciation events or intralacustrine radiation? Our results corroborated previous genetic and ecological studies of these ecotypes, indicating that they represent genetically distinct reproductive units, and therefore refuting the hypothesis of phenotypic polymorphism within a single population. However, the amount of gene flow between ecotypes varied among lakes, correlating with the extent of morphological differentiation and the potential for premating reproductive isolation. The results indicated a polyphyletic origin of ecotypes whereby each of them have been expressed independently more than once. In the two lakes of Squanga Creek drainage, the existence of sympatric pairs was best explained by the secondary contact of two monophyletic whitefish groups that evolved in allopatry during the last glaciation events. In Dezadeash L. of Alsek R. drainage, our results could not verify either sympatric or allopatric (or microallopatric) origin of ecotypes. Regardless of the mode of speciation involved in their origins, these sympatric whitefish populations provided further evidence that Pleistocene glaciation events created conditions favoring rapid divergence and phenotypic differentiation among northern freshwater fishes.
... The goodness of fit tests were conducted by pooling genotypes into three classes with all alleles but the most common considered as one allele because the expected frequencies of some genotypes were so small as to make the standard chisquare test unreliable (Swofford and Selander 1981). Tests of the significance of allele frequency, or genotype frequency for mtDNA, differences between O. nerka from different geographic regions and between sympatric sockeye and kokanee were evaluated using the chi-square randomization procedure outlined by Roff and Bentzen (1989) using the MONTE program of the REAP software package (McElroy et al. 1992). ...
The Pacific salmon Oncorhynchus nerka typically occurs as a sea-run form (sockeye salmon) or may reside permanently in lakes (kokanee) thoughout its native North Pacific. We tested whether such geographically extensive ecotypic variation resulted from parallel evolutionary divergence thoughout the North Pacific or whether the two forms are monophyletic groups by examining allelic variation between sockeye salmon and kokanee at two minisatellite DNA repeat loci and in mitochondrial DNA (mtDNA) Bgl II restriction sites. Our examination of over 750 fish from 24 populations, ranging from Kamchatka to the Columbia River, identified two major genetic groups of North Pacific O. nerka: a "northwestern" group consisting of fish from Kamchatka, western Alaska, and northwestern British Columbia, and a "southern" group consisting of sockeye salmon and kokanee populations from the Fraser and Columbia River systems. Maximum-likelihood analysis accompanied by bootstrapping provided strong support for these two genetic groups of O. nerka; the populations did not cluster by migratory form, but genetic affinities were organized more strongly by geographic proximity. The two major genetic groups resolved in our study probably stem from historical isolation and dispersal of O. nerka from two major Wisconsinan glacial refugia in the North Pacific. There were significant minisatellite DNA allele frequency differences between sockeye salmon and kokanee populations from different parts of the same watershed, between populations spawning in different tributaries of the same lake, and also between sympatric populations spawning in the same stream at the same time. MtDNA Bgl II restriction site variation was significant between sockeye salmon and kokanee spawning in different parts of the same major watershed but not between forms spawning in closer degrees of reproductive sympatry. Patterns of genetic affinity and allele sharing suggested that kokanee have arisen from sea-run sockeye salmon several times independently in the North Pacific. We conclude that sockeye salmon and kokanee are para- and polyphyletic, respectively, and that the present geographic distribution of the ecotypes results from parallel evolutionary origins of kokanee from sockeye (divergences between them) thoughout the North Pacific.
... The statistical significance of tree branches identified by MIX was evaluated by bootstrap resampling ofthe site data with 100 replications using PHYLIP's BOOT program (Felsenstein 1985(Felsenstein , 1990. Estimates of the number of base substitutions per nucleotide site, d (Nei and Miller 1990), and their standard errors (Nei and Tajima 1983) among composite genotypes were calculated using the REAP software package (McElroy et al. 1992). Estimates ofnet sequence divergence between populations, 0, were derived following Nei and Li (1979). ...
The rainbow smelt, Osmerus mordax (Mitchill), is an osmerid fish that exhibits extensive life-history diversity throughout watersheds of northeastern North America. There are both ∗∗∗sea-run (anadromous) and lake-resident (lacustrine) populations and the latter have diversified further into "dwarf-" and "normal-sized" life-history types. Anadromous and lacustrine smelt may inhabit the same watershed and there are several instances where dwarf and normal populations reside within the same lake. We assayed variation among smelt for morphological traits linked to feeding performance in fishes to see if trophic ecology might promote life-history diversity in Osmerus. We also examined mitochondrial DNA (mtDNA) restriction site variation among forms to assess their evolutionary interrelationships. Dwarf smelt had significantly more gill rakers, larger eyes, but shorter upper jaws than normal lake and anadromous smelt. The populations clustered into two trophic "morphotypes"; an anadromous/normal lake group of populations and a group consisting only of dwarf smelt. The mtDNAs of 444 smelt from 16 populations were digested with 12 restriction enzymes revealing 93 composite mtDNA genotypes that clustered (UPGMA) into two major phylogenetic groups differing by 0.78% in sequence. Both genetic groups were present in dwarf and normal smelt as well as in anadromous fish. Further, geographic proximity, rather than trophic morphotype, appeared to be the major determinant of genetic affinities among populations. In two lakes, however, dwarf and normal smelt populations had significantly different mtDNA genotype frequency distributions indicating that the forms are reproductively isolated within both lakes. A clustering analysis of population affinities suggested that the divergence of sympatric dwarf and normal populations had occurred independently in the two lakes. We concluded (1) that trophic ecology is an important factor promoting differentiation in smelt life histories; (2) that smelt ecotypes are polyphyletic and there have been multiple, independent divergences of Osmerus life-history types throughout northeastern North America; and (3) that the biological and mtDNA differences between coexisting dwarf and normal lake smelt argue strongly that their genetic isolation may have developed sympatrically.
... 4), Individual d x y values for each enzyme class were weighted as per Nei and Tajima (1983). Genetic differences between individuals within the same populations (1T) and in different populations (d x y ) were summarized by calculations of the mean nucleotide divergence performed by the program REAP (version 4.0; McElroy et al. 1992). ...
Tropical reef fishes, along with many benthic invertebrates, have a life cycle that includes a sedentary, bottom-dwelling reproductive phase and a planktonic stage that occurs early in development. The adult benthic populations occupy disjunct, patchy habitats; the extent of gene flow due to dispersal of the planktonic life stage is generally unknown.
... The trophic niche of each morphotype was characterized by identifying and enumerating prey items contained in the stomach of each individual. Occurrences of common prey items were compared among morphs with X 2 tests using Monte Carlo simulations (1000 iterations in the REAP package; McElroy et al. 1992). The diet of each fish was also described as the weight proportion of each food item after prey size! ...
Studies on north temperate fish species indicate that new habitat availability following the last ice sheet retreat has promoted ecological speciation in postglacial lakes. Extensive ecophenotypic polymorphisms observed among the North American Great Lakes ciscoes suggest that this fish group has radiated through trophic adaptation and reproductive isolation. This study aims at relating the ecomorphological and genetic polymorphisms expressed by the Lake Nipigon ciscoes to evaluate the likelihood of an intralacustrine divergence driven by the exploitation of alternative resources. Morphological variation and trophic and spatial niches are characterized and contrasted among 203 individuals. Genetic variation at six microsatellite loci is also analyzed to appraise the extent of genetic differentiation among these morphotypes. Ecomorphological data confirm the existence of four distinct morphotypes displaying various levels of trophic and depth niche overlap and specialization. However, ecological and morphological variations were not coupled as expected, suggesting that trophic morphology is not always predictive of ecology. Although extensive genetic variability was observed, little genetic differentiation was found among morphotypes, with only one morph being slightly but significantly differentiated. Contrasting patterns of morphological, ecological, and genetic polymorphisms did not support the hypothesis of ecological speciation: the most ecologically different forms were morphologically most similar, while the only genetically differentiated morph was the least ecologically specialized. The low levels of genetic differentiation and the congruence between θ and φ estimates altogether suggest a recent (most likely postglacial) process of divergence and/or high gene flow among morphs A, C, and D, whereas higher φ estimates for comparison involving morph B suggest that this morph may be derived from another colonizing lineage exchanging little genes with the other morphs. Patterns of ecophenotypic and genetic diversity are also compatible with a more complex evolutionary history involving hybridization and introgression.
... 10.20 and 10.21). All the mtDNA diversity and sequence divergence estimates were calculated using the computer package REAP version 4.0 (McElroy et al. 1992). ...
Restriction fragment length polymorphism analysis of mitochondrial DNA (mtDNA) was used to examine the genetic structure among field voles (Microtus agrestis) from southern and central Sweden. A total of 57 haplotypes was identified in 158 voles from 60 localities. Overall mtDNA diversity was high, but both haplotype and nucleotide diversity exhibited pronounced geographic heterogeneity. Phylogenetic analyses revealed a shallow tree with seven primary mtDNA lineages separated by sequence divergences ranging from 0.6% to 1.0%. The geographic structure of mtDNA diversity and lineage distribution was complex but strongly structured and deviated significantly from an equilibrium situation. The extensive mtDNA diversity observed and the recent biogeographic history of the region suggests that the shallow mtDNA structure in the field vole cannot be explained solely by stochastic lineage sorting in situ or isolation by distance. Instead, the data suggest that the genetic imprints of historical demographic conditions and vicariant geographic events have been preserved and to a large extent determine the contemporary geographic distribution of mtDNA variation. A plausible historical scenario involves differentiation of mtDNA lineages in local populations in glacial refugia, a moving postglacial population structure, and bottlenecks and expansions of mtDNA lineages during the postglacial recolonization of Sweden. By combining the mtDNA data with an analysis of Y-chromosome variation, a specific population unit was identified in southwestern Sweden. This population, defined by a unique mtDNA lineage and fixation of a Y-chromosome variant, probably originated in a population bottleneck in southern Sweden about 12,000 to 13,000 calendar years ago.
... The composite haplotype data and the restriction site matrix were used for subsequent genetic analyses. The REAP software pack- age (Restriction Enzyme Analysis Package; McElroy et al., 1992) was used to derive estimates of haplotype diversity h ( Nei, 1987) and nucleotide diversity π ( Nei and Tajima, 1981) within popula- tions and regions. Whereas between-population diversity was es- timated as net nucleotide sequence divergence d (Nei and Tajima, 1981). ...
The present investigation focuses on population structure analysis of the purple sea urchin Paracentrotus lividus across the African Mediterranean coast, with the main aim of assessing the influence of the Siculo Tunisian Strait on gene flow disruption in this highly dispersive echinoid species. For this purpose, patterns of morphological and genetic variation were assessed among its populations from the western and eastern Mediterranean coasts. A total of 302 specimens from seven Tunisian sites were collected and examined for morphometric variability at twelve morphometric traits. Concordant results, inferred from CDA (canonical discriminant analyses), pairwise NPMANOVA (non parametric multivariate analysis of variance) comparisons and MDS (multidimensional scaling) plot, unveiled significant inter-population differences in the measured traits among the studied populations. Furthermore, the combined use of the one way ANOSIM (analysis of similarities) and the Discriminant/Hotelling analysis allowed unravelling two morphologically differentiated groups assigned to both western and eastern Mediterranean basins. The SIMPER (similarity percentages) routine analysis showed that total dry weight, test diameter and spine length were major contributors to the morphometric separation between locations and between groups. Pattern of phenotypic divergence discerned in P. lividus across the Siculo-Tunisian Strait is interestingly in congruence with that inferred from the genetic investigation of the purple sea urchin populations from the same region based on the analysis of the mtDNA COI (cytochrome oxidase I) gene in 314 specimens from nineteen locations covering a wider geographic transect, streching westward to the Algerian coast and eastward to the Libyan littoral. The specific haplotypic composition characterizing each Mediterranean basin, as inferred from the minimum spanning network, confirmed the geographic partioning of genetic variation, as revealed by F-statistics and AMOVA (analysis of molecular variance) analyses, yielding significant genetic differentiation between eastern and western Mediterranean populations. The newly detected phylogeographic patterns, observed for the first time in P. lividus throughout the explored distribution range, suggest the involvement of different biotic and abiotic processes in shaping such variation, and provide evidence that a large and geographically exhaustive dataset is necessary to unveil phylogeographic structure within widespread marine species, previously cathegorized as panmictic in part of their distribution range.
... Cytochrome b transversion distances were estimated from a phylogeny obtained using CLUSTAL V (Higgins et al. 1992) alignments and PHYLIP (version 3.4; Felsenstein 199 1). The significance of allele frequency differences ' among populations of green and hawksbill turtles was tested by comparing observed x2 values with those obtained from 1,000 randomized data sets (Roff and Bentzen 1989) as implemented in the MONTE routine of REAP (McElroy et al. 1992). ...
Microsatellite loci consisting of (CA)n repetitive arrays were obtained from three species of marine turtle, and primers were designed to test for polymorphism within species and the persistence of microsatellites across species. Homologous loci were found in each test of six marine species within two families (Cheloniidae and Dermochelyidae), as well as in a freshwater species (Emydidae, Trachemys scripta), which indicates a conservation of flanking sequences spanning approximately 300 million years of divergent evolution. The persistence of homologous microsatellites across marine turtles was confirmed by direct sequencing of loci across species and by the discovery of polymorphism in 24 of 30 cross species tests. The conservation of flanking sequences could be due to a slow rate of base substitution in turtle nuclear DNA, as previously reported for mtDNA. In contrast, the presence of up to 25 alleles per locus per species indicates that the replication slippage events responsible for changes in allele length operate as in mammals. Comparisons of alleles among species revealed that alleles of the same length may not be homologous due to mutations within the flanking sequences. Levels of heterozygosity were consistently higher in species from which the primers were designed, which suggests problems with cross-species comparisons of variability. Within species, microsatellite variation between divergent populations was consistent with results from previous mtDNA studies indicating the usefulness of microsatellites for comparing male- versus female-mediated gene flow.
... A parsimony network connecting the observed haplotypes was plotted in TCS version 1.21 software (Clement et al., 2000) to resolve the genealogy. Haplotype diversity (h) and nucleotide diversity (π ) within the populations were estimated according to Nei (1987), based on Kimura's two-parameter distance method using K and DA in the REAP program (McElroy et al., 1993). Pairwise population F ST values were calculated to estimate the genetic differentiation between the populations according to Slatkin & Hudson (1991) using the program Arlequin version 3.0 (Excoffier et al., 2005). ...
We investigated the demographic history of Trinorchestia longiramus Jo, 1988 using the
nucleotide sequence analysis of the mitochondrial cytochrome oxidase subunit I (COI) gene from
277 individuals collected from eight Korean populations. From the low haplotype diversity and
nucleotide diversity in all populations, a neutrality test, and mismatch distribution analysis, the
species appears to have recently experienced a prolonged or severe demographic bottleneck. Pairwise
population FST estimates and AMOVA results showed that substantial differentiation is present
between the southern and eastern populations. The population structure of T. longiramus may have
been influenced by glacial population extinctions and interglacial colonization during the Pleistocene
ice-ages.
... Estimates of nucleotide divergence and dendrogram topology were made using the PAUP version 4.0b10 software package [45]. The main genetic variation indices were estimated using the REAP [46] and ARLEQUIN version 2.0 [28] software packages. Heterogeneity of haplotype frequencies between each sample pair was evaluated using the Monte Carlo method (1000 pseudorandom replicates [47]). ...
The genetic variation and population structure of narrow-clawed crayfish (Astacus leptodactylus) was examined by means of polymerase chain reaction (PCR) restriction fragment length polymorphism (RFLP) analysis of the cytochrome oxidase subunit I (COI) of mitochondrial DNA. A total of 194 adult specimens were collected from seven sample sites including, two in the south Caspian Sea and one each in Anzali wetland and Aras reservoir and three rivers Chafrood, Masule Rudkhan and Siah Darvishan. The PCR products were digested with 19 restriction enzymes and five enzymes revealed polymorphism patterns (DdeІ, MboІ, TaqI, RsaІ and HinfІ). Twenty eight composite haplotypes were showed with the number of haplotypes in each population sample ranging from 8 to 13. Private haplotypes were found at very low frequencies. Two regional (Siah Darvishan River and Astara) groups were clearly recognized by cluster and molecular variance model (AMOVA) analyses (P<0.0001). Each of these groups revealed dominant haplotypes while these haplotypes play less important rule in population structures of the other geographic areas. Intrapopulation haplotype (h) and nucleotide (π) diversities were high for each locality, ranging h=0.7560±0.030 and π= 0.00334±0.00301, respectively. Results of this study discerned two genetically divergent populations of narrow-clawed crayfish including Siah Darvishan River and Astara. Thus, the population structure of the narrow-clawed crayfish, as inferred from mtDNA analysis, is constituted by genetically separate groups that nearly reflect their geographic distribution.
... Annual variation in the allele frequency distributions was evaluated for each probe for three stocks that had been sampled over two years. The chi-square (X 2 ) test with 1,000 Monte Carlo simulations of the distribution of the X 2 statistic (Roff and Bentzen, 1989) was used to evaluate significance of annual variation in allele frequency distributions (McElroy et al., 1992). Genotype frequencies within populations were compared with those expected under Hardy-Weinberg equilibrium by 500 Monte Carlo simulations of the distribution of the X 2 statistic. ...
Geographic variation in minisatellite DNA was examined in 42 stocks of chum salmon, Oncorhynchus keta, from the eastern and western Pacific by restricting genomic DNA with HaeIII and hybridizing it with two minisatellite probes. Regional differentiation in allelic frequencies at the two minisatellite loci was observed; Japanese stocks were distinct from Russian and Yukon River stocks, and stocks from those two regions were distinct from stocks in southeast Alaska and British Columbia. No significant annual variation was observed in allelic frequencies at the two loci for three stocks. Simulated mixed fishery samples of 100 Japanese chum salmon were resolved with a baseline of nine Japanese stocks with an average error of 0.5% per mixture stock. Similarly, simulated mixtures of Yukon River chum salmon resolved with a baseline of five stocks resulted in an average error of 0.6% per mixture stock. Fraser River chum salmon mixtures were resolved with an average error of 3% per mixture stock. With Asian and North American stocks pooled into two groups, accuracy of classification for individual fish to continent of origin was 78% for 323 Asian fish, and 94% for 797 North American fish. Minisatellite DNA variation can be successfully applied to problems of stock discrimination in chum salmon.
... Comparisons of haplotypic frequencies between samples were made with a Monte Carlo χ 2 test and 1000 resamplings using REAP version 4.0 (McElroy et al. 1992). We compared South Africa and Australia and Chile and California at the lowest hierarchical level and three groups, South Africa -Australia, Chile-California, and Japan, at the highest level. ...
Restriction fragment length polymorphism (RFLP) and nucleotide sequence analysis of mitochondrial DNA (mtDNA) have generated conflicting hypotheses on the phylogeography of Indian-Pacific clupeid Sardinops. An RFLP analysis of the control region and adjoining segments indicates a phylogenetic affiliation between southern Africa - Australian and Japanese sardines whereas comparisons of an overlapping segment of the control region sequence indicate an affiliation between southern Africa - Australian and Chile-Californian sardines. An analysis of 258 bp of mtDNA cytochrome b in 74 individuals of Sardinops from South Africa, Australia, Chile, California, and Japan revealed 24 haplotypes, resulting in high levels of haplotypic (h) diversity (average h = 0.70), low levels of nucleotide (pi) diversity (average pi = 0.005), and a satisfactory level of divergence (d) for population resolution (dmax = 4.02%). Cluster and parsimony analyses of haplotypic divergences confirmed the existence of three lineages corresponding to southern Africa - Australia, Chile-California, and Japan but failed to confirm a biogeographic connection between Australia and Japan. These results support the model based on control region sequences and highlight potential pitfalls of RFLP analyses of highly polymorphic DNA sequences with numerous homoplaseous transitions. A comparaison of 220 bp of cytochrome b in samples of Sardina and Sardinops produced an average sequence divergence of 23.2% and supports an ancient divergence between Sardina and Sardinops. The three lineages of Indian-Pacific Sardinops may merit subspecies recognition, based on low but significant levels of mtDNA divergence between them and on evidence of separations between these groups on the order of 200 000 - 500 000 years.
... The χ 2 test with Monte Carlo simulations of the distribution of the χ 2 statistic (Roff and Bentzen 1989) was used to evaluate significance of annual variation in band count or allele frequency distributions, as well as differentiation among regional groupings of stocks. We used 100 simulations of the original data using the MONTE program of the REAP software package (McElroy et al. 1992). Differences in band counts or allele frequencies were used to calculate a generalized squared distance value (D 2 ) (Pimentel 1979) between each pair of stocks. ...
Geographic variation in minisatellite DNA was examined in 28 stocks of chinook salmon (Oncorhynchus tshawytscha) from British Columbia and 3 stocks from the Yukon Territory. Genomic DNA was restricted with the enzymes RsaI and HinfI and hybridized with three minisatellite probes. Regional differentiation in allele frequencies and DNA fragment (band) counts was observed, with stocks from the Fraser River, east coast of Vancouver Island, west coast of Vancouver Island, southern mainland, and northern British Columbia forming distinct groups. With allele frequencies or band counts in the baseline stocks considered fixed or exact, estimates of stock composition from simulated mixtures within the Fraser and Skeena River drainages were accurate and precise, suggesting that discrimination among stocks within river drainages may be possible. Individual chinook salmon were classified with an average accuracy of 35% to stock in a 30-stock baseline and an average accuracy of 65% to region for eight regions. Minisatellite DNA variation offers the potential to accurately and precisely estimate chinook salmon stock composition on a fine geographic scale.
... Estimates of sequence divergence between the haplotypes were calculated from the proportion of shared sites (Nei and Tajima 1983) using a programme described in Palumbi and Wilson (1990). Estimates of nucleotide diversity, the average sequence divergence among individuals, were obtained using the programme REAP (McElroy et al. 1992). The inter-population values were corrected for variation within populations. ...
The hawksbill turtle, Eretmochelys imbricata, is endangered and currently declining in many parts of its global distribution. Efforts to manage the species are hampered by the lack of knowledge of the appropriate geographic units of management and the relationship among breeding populations and feeding assemblages. The Australian populations are among the few remaining large assemblages in the world, but may be under threat from harvesting in neighbouring countries. We use patterns of mitochondrial DNA variation to determine the geographic scale of breeding populations and to compare the genetic composition of turtles in feeding populations to those nesting at nearby major rookeries. Four of the major Australian rookeries were sampled, two on the western coast and two in northeastern Australia, as were turtles at two foraging sites. Significant differences in the frequency of two divergent mitochondrial DNA types separated the turtles nesting at major rookeries sampled on the northeastern versus western coasts of Australia, demonstrating that these populations are not connected by significant amounts of gene flow and should be considered as separate entities for management. There was no significant difference between the turtles nesting at two western rookeries 100 km apart, nor between those using the two northeastern rookeries separated by 750 km. This indicates that the size of the interbreeding unit for the hawksbill turtle is likely to be a region consisting of a group of islands rather than an individual island. Feeding populations were screened with a gene amplification test that discriminates between the two major DNA types. In each case, there was a significant difference in allele frequency between feeding populations and the nearest major rookery. This, together with previous reports of long distance migrations from tag returns, suggests that individual foraging areas support hawksbill turtles from distant breeding populations.
... Variable characters among taxa included base substitutions (transitions and transversions) and insertions and deletions (indels). Levels of inter-and intra-population genetic diversity were quantified by haplotype diversity (h) (Nei and Tajima 1983) and the average number of nucleotide substitutions per nucleotide site within (nucleotide diversity (π) (Nei 1987) and among populations (nucleotide divergence (d xy ) (Nei and Tajima 1983), based on the entire data set using the program DA2 in restriction enzyme analysis package (REAP) version 5.0 (McElroy et al. 1992;McElroy 1997). Differences in nucleotide substitution frequencies among species were tested with chi-square contingency table tests (Sokal and Rohlf 1995). ...
... The main indices of genetic variation were evalu ated using the REAP [22] and ARLEQUIN v. 2.0 [23] software programs. Heterogeneity of the haplotype frequencies between the pairs of samples examined was tested using the Monte Carlo analysis (17000 pseudoran dom replicates) [24] with the CHIRXC program [25]. ...
... However, in the present study computations were made using refined mapping data for the amplified DNA fragments. The main indices of genetic variation were evaluu ated using the REAP [22] and ARLEQUIN v. 2.0 [23] software programs. Heterogeneity of the haplotype frequencies between the pairs of samples examined was tested using the Monte Carlo analysis (17000 pseudoran dom replicates) [24] with the CHIRXC program [25]. ...
... We calculated haplotype frequencies using REAP (version 4 (McElroy et al. 1992)) and used both Monte Carlo simulation (in REAP) and the R3C test to search for significant differences in haplotype frequencies among collections and subpopulations. Haplotypes other than the common haplotype were combined for the R 3 C tests. ...
Knowledge of changes in the interdependence of a speciesÕ populations for continued existence (connectivity) and of the forces driving connectivity patterns is critical for management and conservation of the species. Population genetics can be used to investigate population connectivity. Combining population genetics with climatic, environmental, and biological (external) factors that can influence population structure and connectivity can lead to a greater understanding of the forces influencing population dynamics. We deciphered the population genetic structure and connectivity patterns of bay scallops (Argopecten irradians concentricus Lamarck) from Florida Gulf of Mexico waters using allozyme-locus and mitochondrial DNA population genetics data from samples representing four consecutive generations. We evaluated bay scallop population genetic relationships within the context of habitat, hydrodynamic, and environmental variation, and concomitant spatial patterns in the abundance of adult and recently recruited scallops to infer the influence of these factors on bay scallop population structure. Florida Gulf bay scallops form a hierarchical, mixed-model, source–sink metapopulation with intergenerational variation in connectivity that seems to be influenced by the factors we considered. An El Ninõ event that occurred during 1 y caused climatic and environmental change that greatly reduced subpopulation connectivity, allowing us to understand more completely the potential relative importance of the other external factors on change in metapopulation connectivity over time. Our study illustrates the value of using multiple genetic markers, sampling for multiple years, and integrating data from multiple external factors for understanding the population genetic structure of species for adaptive management.
... PCR products (approximately 500 base pairs) were incubated overnight with 10 U of Nsi I at 37ЊC, and the products were visualized under ultraviolet light on 2.5% agarose gels stained with ethidium bromide or SyberGreen (Molecular Probes, Inc., Eugene, OR). We tested for differences in clade frequencies among the collections using Monte Carlo chi-square permutations (Roff and Bentzen 1989) as implemented in Monte of the REAP software package (McElroy et al. 1992). ...
We investigated the interplay between natural selection and gene flow in the adaptive divergence of
threespine stickleback (Gasterosteus aculeatus) that reside parapatrically in lakes and streams. Within the Misty Lake
system (Vancouver Island, British Columbia), stickleback from the inlet stream (flowing into the lake) have fewer
gill rakers and deeper bodies than stickleback from the lake—differences thought to facilitate foraging (benthic
macroinvertebrates in the stream vs. zooplankton in the open water of the lake). Common-garden experiments demonstrated
that these differences have a genetic basis. Reciprocal transplant enclosure experiments showed that lake
and inlet stickleback grow best in their home environments (although differences were subtle and often not significant).
Release-recapture experiments in the inlet showed that lake fish are less well-suited than inlet fish for life in the
stream (higher mortality or emigration in lake fish). Morphological divergence in the wild and under common rearing
was greater between the lake and the inlet than between the lake and the outlet. Genetic divergence (mitochondrial
DNA and microsatellites) was greatest between the lake and the upper inlet (1.8 km upstream from the lake), intermediate
between the lake and the lower inlet (0.9 km upstream), and least between the lake and the outlet stream
(1.2 km downstream). Relative levels of gene flow estimated from genetic data showed the inverse pattern. The
negative association between morphological divergence and gene flow is consistent with the expectation that gene
flow can constrain adaptation. Estimated absolute levels of gene flow also implied a constraint on adaptation in the
outlet but not the inlet. Our results suggest that natural selection promotes the adaptive divergence of lake and stream
stickleback, but that the magnitude of divergence can be constrained by gene flow.
... Sequence divergences were computed by using the pairwise-deletion option in MEGA; this distance estimator excludes sites at which indels occur on a pairwise basis. Haplotype and nucleotide diversity within samples and nucleotide divergence (D) between pairs of samples were estimated according to Nei and Tajima (1981) and by using the DAoption of REAP 4.0 (McElroy et al., 1992). The nucleotide divergence values were clustered by using the NJTREE program (Jin and Ferguson, 1990) based on the neighbor-joining method of Saitou and Nei (1987). ...
Genetic information pertaining to stock structure in red drum (Sciaenops ocellatus) is equivocal, complicating attempts to develop sound fishery management and stock enhancement plans. In this study, genetic stock structure was examined by using mitochondrial DNA (mtDNA) control region sequences of 209 individual red drum from six locations in the Gulf of Mexico and five locations in the nearshore Atlantic Ocean off the southeastern United States. Eighty-one polymorphic sites within a 369 base-pair portion of the control region defined 134 different haplotypes which differed by up to 26 nucleotide substitutions. Red drum showed high average within-sample haplotype (0.98) and nucleotide (0.030) diversities. Sequence divergences between pairs of haplotypes ranged from 0.27% to 7.06% (x̄=3.17%). Cluster analysis of haplotypes revealed very little phylogeographic structure among mtDNA lineages. However, a neighbor-joining tree based on nucleotide divergence between pairs of samples showed cohesion among Atlantic samples and, to a lesser degree, among Gulf samples. In contrast to a prior study, we found no evidence that red drum in Mosquito Lagoon, Florida, constitute a self-contained, reproductively isolated population. Hierarchical analysis of molecular variance supported the hypothesis that red drum are subdivided into two weakly diverged populations with a genetic transition in south Florida between Sarasota Bay and Mosquito Lagoon. This area forms a zone of differentiation between two genetically semi-isolated populations between which the structuring of heterogeneity differs from that under the assumption of panmixia. In addition, the analysis of molecular variance also indicated that red drum from Apalachicola Bay are genetically divergent from all other samples. The Atlantic and Gulf red drum populations are likely to respond independently to harvest regulations; these fisheries should continue to be managed separately. Additional subdivision of the Gulf stock between peninsular Florida and the northern and western Gulf may also be warranted.
... Clustering and ordination were achieved by using NTSYS 1.6 (Rohlf 1990). Input files for all analyses were constructed by using REAP (McElroy et al. 1992). ...
Molecular genetic variation was examined within and among species of the rock-dwelling cichlid fishes (mbuna) of Lake Malawi. Phylogenetic relationships among mbuna mitochondrial DNA (mtDNA) haplotypes were estimated by using restriction-fragment-length polymorphisms. The distribution of these lineages among mbuna species is of particular significance for phylogenetic systematic study of this fauna. Some species were found to be polymorphic for divergent haplotypes that substantially predate their isolation from sister taxa. Repeated speciation events among numerous closely related taxa appear to have been so recent that mtDNA lineage sorting among species is incomplete. Thus, the mtDNA gene tree is not congruent with the putative species tree. These results indicate that analysis of mtDNA alone will not be sufficient for resolution of phylogenetic relationships in the mbuna. Clarification of these relationships will require examination of multiple nuclear loci, because many of these new markers are also likely to retain ancestral polymorphisms.
... The data on the sizes of the restriction fragments and the composition of combined haplotypes can be obtained from the authors upon request. Statistical treatment of the data was performed using the MRBAYES version 3.2 [19], PAUP version 4.0b10 [20], PHYLIP 3.67 [21], and REAP [22] software packages. ...
Charrs of the genus Salvelinus (including Salvethymus) represent a monophyletic group of salmonid fishes that diverged from the common ancestor without subdivision into subgenera. The phylogenesis of the genus is characterized by four cycles of mitochondrial genome divergence. The first one, belonging to the Late Miocene—the border between Miocene and Pliocene (6 to 4 million years ago)—was associated with the consecutive divergence of the S. fontinalis, S. namaycush, S. levanidovi, and S. leucomaenis basal branches. Two divergence events, including separation of the ancestral lineage of Western Pacific group of S. m. krascheninnikovi and the following segregation of the common ancestor into two mitochondrial phyla, happened within the period of 3 to 2 million years ago. The next cycle is attributed to the time interval of about 1 million years ago and includes the divergence of both phyla. In one phylum, a relatively quick isolation of Arctic and Eastern Pacific phylogroups, along with the divergence of the latter phylogroup into S. confluentus and S. m. lordi lineages, took place. At the same time, the second phylum diverged into the S. m. malma and S. alpinus phylogenetic groups. At the final stage (Middle to Late Pleistocene), differentiation of the taxa within the phylogenetic groups took place.
... Standard measures of genetic variation within samples, including allelic frequency, observed heterozygosity (H o ), expected heterozygosity (H e ), and assessment of Hardy-Weinberg equilibria, were calculated using the GENEPOP program version 1.2 (Raymond and Rousset 1995). The homogeneity of allelic frequencies among samples was evaluated using χ 2 randomization tests (Roff and Bentzen 1989) with 1000 permutations performed by the Monte program of the REAP software package (McElroy et al. 1992). ...
The principal objective of this study was to describe the pattern of genetic exchange and isolation of Atlantic salmon (Salmo salar) populations among geographical regions of the province of Quebec, Canada. Seven riverine populations, associated with three putative regional metapopulations (North Shore, Gaspe Peninsula, and Ungava), were analyzed using microsatellites. Our results did not support the putative metapopulation structure. Significant heterogeneity in allelic frequency was observed among most rivers independently of their location or group subdivision. Interpopulation genetic variance (φ(ST)) indicates less heterogeneity among rivers than χ2 analysis and was mainly associated with the geographical distance of the most isolated rivers, the Natashquan and the Koksoak. Even with low genetic variance among populations, the overall significant allelic heterogeneity among rivers strongly suggests that each population, whether separated by thousands or tens of kilometres, should be considered and managed as a specific stock.
Silver carp (Hypophthalmichthys molitrix), grass carp (Ctenopharyngodon piceus), bighead carp (Aristichthys nobilis), and black carp (Mylopharyngodon piceus) rank first, second, fourth, and seventh in world fish production. In China, the Yangtze River harbours the most important natural populations of these species. We performed a polymerase chain reaction restriction fragment length poymorphism analysis on 365 juvenile fish representing three nursery grounds to provide a first assessment of the mitochondrial DNA diversity in these species and test the hypothesis that they are composed of more than one genetic stock. The mitochondrial DNA diversity was high in silver, bighead, and black carp, and much less in grass carp. Analysis of heterogeneity of genotype frequency, fixation indices, intersite molecular variance, and localization indices indicated that juvenile silver, bighead, and black carp from different nursery areas belong to genetically distinct populations. These results suggest that their population structure may be determined by the number of environmental settings that permit closure of their life cycle. They also imply that carp from the Yangtze River cannot be managed as a single unit and that human disturbance through exploitation and habitat modifications, in particular the construction of the Three Gorges Dam, will have differential impacts on fish abundance for different parts of the river.
We analyzed the genetic diversity and structure of three allopatric populations of the Pacific red snapper Lutjanus peru (Nichols and Murphy, 1922) by means of restriction fragment length polymorphisms of the entire mitochondrial control region (1350 bp). We found high levels of haplotype (h = 0.966) and nucleotide (π = 3.23%) diversities among the 100 organisms analyzed from Baja California Sur, Sinaloa and Jalisco (Mexico). Most of the molecular variability was detected with only one of the five restriction enzymes used (MseI). Heterogeneity analysis of haplotype frequencies was not significant (X² = 125.1, P > 0.25); neither were Wright's fixation index (F ST = 0.0062, P = 0.140) nor its molecular analogue (Φst = 0.0194, P = 0.056). An analysis of molecular variance (AMOVA) confirmed the absence of differentiation between peninsular and continental populations, even though it produced a marginally significant Φst (Φst = 0.0116, P = 0.048). No phylogeographic pattern was detected in a Neighbor-Joining gene tree. We argue that high molecular diversity levels are consistent with a large population size and that the absence of an apparent genetic structure, in the extreme north of the species distribution, suggests the action of mechanisms favoring passive larval transport among allopatric populations; although active adult migration cannot be ruled out.
Both mtDNA variation and allozyme data demonstrate that geographic groupings of different color morphs of the starfish Linckia laevigata are congruent with a genetic discontinuity between the Indian and Pacific Oceans. Populations of L. laevigata sampled from Thailand and South Africa, where an orange color morph predominates, were surveyed using seven polymorphic enzyme loci and restriction fragment analysis of a portion of the mtDNA including the control region. Both allozyme and DNA data demonstrated that these populations were significantly genetically differentiated from each other and to a greater degree from 23 populations throughout the West Pacific Ocean, where a blue color morph is predominant. The genetic structure observed in L. laevigata is consistent with traditional ideas of a biogeographic boundary between the Indian and Pacific Oceans except that populations several hundreds kilometers off the coast of north Western Australia (Indian Ocean) were genetically similar to and had the same color morphs as Pacific populations. It is suggested that gene flow may have continued (possibly at a reduced rate) between these offshore reefs in Western Australia and the West Pacific during Pleistocene falls in sea level, but at the same time gene flow was restricted between these Western Australian populations and those in both Thailand and South Africa, possibly by upwellings. The molecular data in this study suggest that vicariant events have played an important role in shaping the broadscale genetic structure of L. laevigata. Additionally, greater genetic structure was observed among Indian Ocean populations than among Pacific Ocean populations, probably because there are fewer reefs and island archipelagos in the Indian Ocean than in the Pacific, and because present-day surface ocean currents do not facilitate long-distance dispersal.
We performed a phylogenetic analysis of mtDNA variation among seven sympatric pairs of dwarf and normal morphotypes of whitefish from northern Québec and the St. John River drainage to address three questions relevant to understanding their radiation. Are all sympatric pairs reproductively isolated? Do phylogenetic analyses confirm that sympatric whitefish morphotypes found in eastern North America represent the outcome of polyphyletic evolutionary events? If so, did all sympatric pairs from the St. John River drainage originate from the same scenario of allopatric divergence and secondary contact? The hypothesis of genetic differentiation was supported for all sympatric pairs from the St. John River drainage, whereas lack of mtDNA diversity precluded any test of reproductive isolation for northern Québec populations. Patterns of mtDNA variation confirmed that dwarf and normal morphotypes evolved in parallel among independent, yet closely related, lineages, thus providing indirect evidence for the role of natural selection in promoting phenotypic radiation in whitefish. Patterns of mtDNA diversity among sympatric pairs of the St. John River indicated a complex picture of whitefish evolution that implied sympatric divergence and multiple allopatric divergence/secondary contact events on a small geographic scale. These results suggests that ecological opportunities, namely trophic niche availability, may promote population divergence in whitefish.
Sardines (Sardinops spp.) occupy temperate upwelling zones in the coastal regions of the Indian and Pacific Oceans, including locations in Japan, California, Chile, Australia, and South Africa. East and West Pacific populations are separated by vast expanses of open ocean, and northern and southern hemisphere populations are separated by tropical waters which are lethal to sardines. The relative importance of these barriers has been the focus of a longstanding debate between vicariance and dispersal schools in biogeography. Comparisons of a 500 bp fragment of the mitochondrial (mt) DNA control region reveal strong geographic structuring of mtDNA lineages but shallow divergence both within and between regional populations. Regional populations are related to one another in a stepping-stone pattern, the apparent result of a series of Pleistocene dispersal events around the continental margins of the Indian-Pacific Basin. These mtDNA data, combined with an electrophoretic survey of variability at 34 nuclear loci (Grant and Leslie 1996), indicate that the five regional forms of Sardinops (considered separate taxa by most authorities) probably diverged within 500,000 years BP, a much shorter timeframe than predicted by vicariance models based on plate tectonics. High mtDNA haplotype diversity, coupled with an excess of rare alleles in the protein electrophoretic dataset, may indicate exponential growth from a small ancestral population. The mtDNA and allozyme data are concordant with climate records and fossil evidence in portraying regional populations as recent, unstable, and ephemeral. Regional populations of sardines have probably been extinguished and recolonized over short evolutionary timescales in response to changes in climate and the oceanography of coastal upwelling zones.
Geographic patterns of genetic variation (mitochondrial DNA [mtDNA] and allozymes) were used to examine effects of intrinsic characteristics (e.g., vagility, habitat specificity, and reproductive behaviors) and extrinsic factors (e.g., climatic and geological history) on population fragmentation. The three species of cyprinid fishes examined (Tiaroga cobitis, Meda fulgida, and Agosia chrysogaster) occupied similar historical ranges within the lower Colorado River drainage, but differ in intrinsic characteristics conducive to population fragmentation. Relationships among populations were similar across species, reflecting common historical influences, but results indicate the distribution of variation among species is strongly affected by intrinsic characteristics. Variation within two species (T. cobitis and M. fulgida) is subdivided among populations, suggesting little gene flow among rivers. In contrast, similarity of A. chrysogaster populations throughout the Gila River drainage supports the hypothesis that levels of gene flow are high for this species. Levels of mtDNA divergence were much higher than expected for both T. cobitis and A. chrysogaster suggesting long-term isolation of geographic regions. These results indicate that both long-term and short-term extrinsic factors have shaped basic patterns of variation within these fishes; however, the intrinsic characteristics of each species have strongly affected the population genetic structure of these fishes.
We analyzed mitochondrial DNA (mtDNA) restriction-site variation in bananaquit (Coereba flaveola; Aves, Coerebinae) populations sampled on 12 Caribbean islands and at 5 continental localities in Central America and northern South America. Multiple fixed restriction-site differences genetically defined several regional bananaquit populations. An mtDNA clade representing all Jamaican bananaquits was the most divergent; the estimated average sequence divergence (dxy ) between Jamaican and all other mtDNA haplotypes surveyed was 0.027. Three groups of populations, representing Central America, northern South America, and the eastern Antilles (Puerto Rico to Grenada) were nearly equally differentiated among themselves (average dxy = 0.014), and may represent a single, recent range expansion. Within the eastern Antilles, three geographically restricted haplotype groups were identified: Puerto Rico, north-central Lesser Antilles (U.S. Virgin Islands to St. Lucia), and Grenada-St. Vincent. The evolutionary relationships of these groups were not clear. Genetic homogeneity of the island populations from the U.S. Virgin Islands to St. Lucia suggested a recent spread of a specific north-central Lesser Antillean haplotype through most of those islands. Haplotype variation across this region indicated that this spread may have occurred in two waves, first through the southernmost islands of St. Lucia, Martinique, and Dominica, and more recently from Guadeloupe to the north. The geographic distribution of mtDNA haplotypes, and of bananaquit populations, suggests periods of invasiveness followed by relative geographic quiescence. Although most genetic studies of bird populations have revealed homogeneity over large geographic areas, our findings provide a remarkable counterexample of strong geographic structuring of mtDNA variation over relatively small distances. Furthermore, although the mtDNA data were consistent with several subspecific distinctions, it was clear that named subspecies do not define equally differentiated evolutionary entities.
Genetic variation and population differentiation of Apis cerana in Thailand were examined by restriction analysis of amplified mitochondrial srRNA and IrRNA genes, and the intergenic CO1-CO2 region with Dral. Twelve composite haplotypes were found from 170 colonies investigated. Large genetic differences were observed among A. cerana populations from northern and peninsular Thailand. The population from Samui Island was distinct, whereas A. cerana from Phuket Island was genetically similar to that from peninsular Thailand. Geographic heterogeneity analysis and FST estimates indicated a high level of population subdivision in this species (P < 0.0001 and FST = 0.604). Using percent sequence divergence as a measure of genetic distance, three distinct groups were found using the clustering algorithm UPGMA. These were: north Thailand (A), peninsular Thailand, and Phuket (B) and Samui Islands
We used restriction fragment length polymorphism (RFLP) analysis of mitochondrial DNA (mtDNA) diversity to assess the complex postglacial history of lake trout (Salvelinus namaycush) and test existing dispersal hypotheses. A pilot survey with 30 restriction enzymes was carried out on lake trout from 16 geographically representative populations to determine phylogenetically informative characters. Subsequent screening of 1416 lake trout from 93 populations across the species' range with nine variable restriction enzymes showed that lake trout from at least five glacial refugia contributed to extant populations. Three major mtDNA lineages were observed, with sufficient differences to suggest their divergence during the mid-Pleistocene. Geographic and genetic differences within two lineages suggested further vicariant divergence caused by Wisconsinan glacial advances. In contrast with more southern freshwater species, no correlation was observed between the geographic proximity of glacial refugia and relatedness of mtDNA lineages. Current distributions of refugial lineages are readily explained by consideration of timing and connections of proglacial lakes. These lakes facilitated large-scale dispersal from multiple refugia, particularly enabling long-distance dispersal from the Mississippian and northwestern refugia. Proglacial lakes also enabled extensive secondary contact among refugial groups, resulting in high levels of intrapopulation mtDNA diversity within their former boundaries.
Comparison of sequences among vertebrates shows that both relatively fast and slowly evolving areas lie within the mtDNA control region. Comparison has been made between the genetic divergence of mtDNA control region sequences within and among closely related species and genera in the teleost fish family Percidae. Gene trees from control region data are compared to morphology-based phylogenies and population genetic statistics are compared to hypotheses of population structure derived from geological evidence and tagging studies. It details the morphological evolution and genetics of the Percidae. The evolutionary methods used for these studies include collection of specimens, genetic analysis, and data analysis. The results of these analyses show that the utility of mtDNA sequences for population genetics and biogeography for several taxa of bony fishes indicate that mtDNA control regions of other teleosts may evolve at similarly rapid rates. It is expected that mtDNA control region sequences will continue to prove valuable for elucidating within-species and congeneric relationships.
Bay scallops (Argopecten irradians Lamarck) are ecologically important in U.S. Atlantic waters off northeastern states and in the Florida Gulf of Mexico, and have been intensely harvested from both of those regions for decades. However, a detailed study comparing their basic population genetic structures using more than a single type of genetic marker has not been conducted. Through such a study, key phylogeographic, taxonomic, and fisheries issues can be addressed. We used variation in allozyme loci and mitochondrial DNA restriction fragment length polymorphisms to evaluate and compare the population genetic structures of bay scallops from those two regions, to propose a new interpretation for the composition of the North Carolina bay scallop population, to resolve the taxonomic quandary of Argopecten irradians taylorae, and to evaluate the apparent and potential genetic effects of the common fishery practice of hatchery-based stock enhancement on the genetic diversity and relatedness of Atlantic bay scallop populations. Atlantic Ocean (North Carolina through New York) bay scallop populations are genetically more distant from each other than are Florida Gulf bay scallop populations, except those in Florida Bay. Each Atlantic population has a different phylogeographic history, is quasi-independent, and should be treated as a genetically unique entity. The North Carolina bay scallop population is composed of Argopecten irradians irradians individuals, but also has genetic input from Argopecten irradians concentricus. Bay scallops occurring in Florida Bay constitute a population of A. i. concentricus that has diverged from other Florida Gulf populations because it has undergone repeated contractions and expansions of varying magnitude and is nearly isolated from other bay scallop populations. For the common practice of hatchery-based stock enhancement in the Atlantic, broodstock bay scallops should be taken from the same genetic population, and all stock enhancement efforts should include comprehensive genetic monitoring programs. In some cases, improving the abundance and density of bay scallop aggregations through habitat improvement may be preferable to stock enhancement for bay scallop restoration, but in other cases genetically conscientious stock supplementation or restoration may be the only alternative.
ResearchGate has not been able to resolve any references for this publication.