Andrey Tatarenkov

ALLOZYME VARIATION IN A SNAIL (LITTORINA SAXATILIS) : DECONFOUNDING THE EFFECTS OF MICROHABITAT AND GENE FLOW

It is commonly observed that a restricted gene flow among populations of a species generates genetic differentiation in, for example, allozyme markers. However, recent studies suggest that microhabitat‐specific variation may contribute to the total differentiation. To appreciate the relative contributions of geographic variation and habitat‐specific variation, we sampled 42 subpopulations of the intertidal snail Littorina saxatilis from three different microhabitats (boulders, low and high rocky intertidal) on five small islands within a distance of 15 km. We used a modified orthogonal version of Neis gene diversity analysis with a modified analysis of variance (ANOVA) that estimated the significance of habitat and geographic separation and the interaction between them. Between subpopulation differentiation (GST) was usually in the range of 5% to 10% but was exceptionally high in one locus (Aat; 53%). Genetic differentiation attributable to different habitats accounted for 10% to 81% (mean 35%) of the between subpopulation variation and was significant (P < 0.05) in six loci. Differentiation due to geographic separation accounted for 11% to 61% (mean 36%) and was significant (P < 0.05) in seven loci. Furthermore, three loci showed interactions between habitat and island, suggesting varying effects of habitat in different islands. Microhabitat‐specific variation, probably through spatially varying fitness, seems particularly likely in Aat and Pgm‐2. Moderate levels of habitat associated variation added to the observed differentiation due to gene flow in Pgi, Pnp, and Pgm‐1, whereas in the remaining three loci either the habitat effect was confused by strong habitat‐island interaction (Ark) or was virtually absent (Pep and Mpi).

ON THE EVOLUTION OF DOPA DECARBOXYLASE (DDC) AND DROSOPHILA SYSTEMATICS

Abstract. We have sequenced most of the coding region of the gene Dopa decarboxylase (Ddc) in 24 fruitfly species. The Ddc gene is quite informative about Drosophila phylogeny. Several outstanding issues in Drosophila phylogeny are resolved by analysis of the Ddc sequences alone or in combination with three other genes, Sod, Adh, and Gpdh. The three species groups, melanogaster, obscura, and willistoni, are each monophyletic and all three combined form a monophyletic group, which corresponds to the subgenus Sophophora. The Sophophora subgenus is the sister group to all other Drosophila subgenera (including some named genera, previously considered outside the Drosophila genus, namely, Scaptomyza and Zaprionus, which are therefore downgraded to the category of subgenus). The Hawaiian Drosophila and Scaptomyza are a monophyletic group, which is the sister clade to the virilis and repleta groups of the subgenus Drosophila. The subgenus Drosophila appears to be paraphyletic, although this is not definitely resolved. The two genera Scaptodrosophila and Chymomyza are older than the genus Drosophila. The data favor the hypothesis that Chymomyza is older than Scaptodrosophila, although this issue is not definitely resolved. Molecular evolution is erratic. The rates of nucleotide substitution in 3rd codon position relative to positions 1 + 2 vary from one species lineage to another and from gene to gene.

Rapid concerted evolution in animal mitochondrial DNA

Recombinational genetic processes are thought to be rare in the uniparentally inherited mitochondrial (mt) DNA molecules of vertebrates and other animals. Here, however, we document extremely rapid concerted microevolution, probably mediated by frequent gene conversion events, of duplicated sequences in the mtDNA control region of mangrove killifishes (Kryptolebias marmoratus). In local populations, genetic distances between paralogous loci within an individual were typically smaller (and often zero) than those between orthologous loci in different specimens. These findings call for the recognition of concerted evolution as a microevolutionary process and gene conversion as a likely recombinational force in animal mtDNA. The previously unsuspected power of these molecular phenomena could greatly impact mtDNA dynamics within germ cell lineages and in local animal populations.

A mixed-mating strategy in a hermaphroditic vertebrate

Mixed-mating systems, in which hermaphrodites can either self-fertilize or outcross, are common in many species of plants and invertebrates and have been informative models for studying the selective forces that can maintain both inbreeding and outbreeding in populations. Here, we document a remarkable instance of evolutionary convergence to an analogous mixed mating system by a vertebrate, the mangrove killifish (Kryptolebias marmoratus). In this androdioecious species, most individuals are simultaneous hermaphrodites that characteristically self-fertilize, resulting in local populations that consist of (nearly) homozygous lines. Most demes are also genetically diverse, an observation traditionally attributed to de novo mutation coupled with high levels of inter-site migration. However, data presented here, from a survey of 35 microsatellite loci in Floridian populations, show that genotypic diversity also stems proximally from occasional outcross events that release ‘explosions’ of transient recombinant variation. The result is a local population genetic pattern (of extensive genotypic variety despite low but highly heterogeneous intra-individual heterozygosities) that differs qualitatively from the genetic architectures known in any other vertebrate species. Advantages of a mixed-mating strategy in K. marmoratus probably relate to this fishs solitary lifestyle and its ability to colonize new habitats.

GENETIC STRUCTURE IN POPULATIONS OF FUCUS VESICULOSUS (PHAEOPHYCEAE) OVER SPATIAL SCALES FROM 10 M TO 800 KM1

Recent studies showing consequences of species’ genetic diversity on ecosystem performance raise the concern of how key ecosystem species are genetically structured. The bladder wrack Fucus vesiculosus L. is a dominant species of macroalga in the northern Atlantic, and it is particularly important as a habitat‐forming species in the Baltic Sea. We examined the genetic structure of populations of F. vesiculosus with a hierarchical approach from a within‐shore scale (10 m) to a between‐seas scale (Baltic Sea–Skagerrak, 800 km). Analysis of five microsatellite loci showed that population differentiation was generally strong (average FST = 12%), being significant at all spatial scales investigated (101, 103, 104–5, 106 m). Genetic differentiation between seas (Baltic Sea and Skagerrak) was substantial. Nevertheless, the effects of isolation by distance were stronger within seas than between seas. Notably, Baltic summer‐reproducing populations showed a strong within‐sea, between‐area (70 km) genetic structure, while Baltic autumn‐reproducing populations and Skagerrak summer‐reproducing populations revealed most genetic diversity between samples within areas (<1 km). Despite such differences in overall structure, Baltic populations of summer‐ and autumn‐reproducing morphs did not separate in a cluster analysis, indicating minor, if any, barriers to gene flow between them. Our results have important implications for management and conservation of F. vesiculosus, and we raise a number of concerns about how genetic variability should be preserved within this species.

Effects of Pleistocene climatic fluctuations on the phylogeographic and demographic histories of Pacific herring (Clupea pallasii)

We gathered mitochondrial DNA sequences (557 bp from the control region in 935 specimens and 668 bp of the cytochrome b gene in 139 specimens) of Pacific herring collected from 20 nearshore localities spanning the species’ extensive range along the North Pacific coastlines of Asia and North America. Haplotype diversity and nucleotide diversity were high, and three major phylogeographic lineages (sequence divergences ca. 1.5%) were detected. Using a variety of phylogenetic methods, coalescent reasoning, and molecular dating interpreted in conjunction with paleoclimatic and physiographic evidence, we infer that the genetic make‐up of extant populations of C. pallasii was shaped by Pleistocene environmental impacts on the historical demography of this species. A deep genealogical split that cleanly distinguishes populations in the western vs. eastern North Pacific probably originated as a vicariant separation associated with a glacial cycle that drove the species southward and isolated two ancestral populations in Asia and North America. Another deep genealogical split may have involved either a vicariant isolation of a third herring lineage (perhaps originally in the Gulf of California) or it may have resulted simply from the long coalescent times that are possible in large populations. Coalescent analyses showed that all the three evolutionary lineages of C. pallasii experienced major expansions in their most recent histories after having remained more stable in the preceding periods. Independent of the molecular calibration chosen, populations of C. pallasii appear to have remained stable or grown throughout the periods that covered at least two major glaciations, and probably more.

Genetic Composition of Laboratory Stocks of the Self-Fertilizing Fish Kryptolebias marmoratus: A Valuable Resource for Experimental Research

The hermaphroditic Mangrove Killifish, Kryptolebias marmoratus, is the worlds only vertebrate that routinely self-fertilizes. As such, highly inbred and presumably isogenic “clonal” lineages of this androdioecious species have long been maintained in several laboratories and used in a wide variety of experiments that require genetically uniform vertebrate specimens. Here we conduct a genetic inventory of essentially all laboratory stocks of the Mangrove Killifish held worldwide. At 32 microsatellite loci, these stocks proved to show extensive interline differentiation as well as some intraline variation, much of which can be attributed to post-origin de novo mutations and/or to the segregation of polymorphisms from wild progenitors. Our genetic findings also document that many of the surveyed laboratory strains are not what they have been labeled, apparently due to the rather frequent mishandling or unintended mixing of various laboratory stocks over the years. Our genetic inventory should help to clarify much of this confusion about the clonal identities and genetic relationships of laboratory lines, and thereby help to rejuvenate interest in K. marmoratus as a reliable vertebrate model for experimental research that requires or can capitalize upon “clonal” replicate specimens.

Pronounced reproductive skew in a natural population of green swordtails, Xiphophorus helleri

For many species in nature, a sires progeny may be distributed among a few or many dams. This poses logistical challenges — typically much greater across males than across females — for assessing means and variances in mating success (number of mates) and reproductive success (number of progeny). Here we overcome these difficulties by exhaustively analyzing a population of green swordtail fish (Xiphophorus helleri) for genetic paternity (and maternity) using a suite of highly polymorphic microsatellite loci. Genetic analyses of 1476 progeny from 69 pregnant females and 158 candidate sires revealed pronounced skews in male reproductive success both within and among broods. These skews were statistically significant, greater than in females, and correlated in males but not in females with mating success. We also compare the standardized variances in swordtail reproductive success to the few such available estimates for other taxa, notably several mammal species with varied mating systems and degrees of sexual dimorphism. The comparison showed that the opportunity for selection on male X. helleri is among the highest yet reported in fishes, and it is intermediate compared to estimates available for mammals. This study is one of a few exhaustive genetic assessments of joint‐sex parentage in a natural fish population, and results are relevant to the operation of sexual selection in this sexually dimorphic, high‐fecundity species.

Long-term retention of self-fertilization in a fish clade

Among vertebrate animals, only the mangrove rivulus (Kryptolebias marmoratus) was known to self-fertilize. Here, we use microsatellite analyses to document a high selfing rate (97%) in a related nominal species, Kryptolebias ocellatus, which likewise is androdioecious (populations consist of males and hermaphrodites). In contrast, we find no evidence of self-fertilization in Kryptolebias caudomarginatus (an androdioecious species closely related to the marmoratus-ocellatus clade) or in Kryptolebias brasiliensis (a dioecious outgroup). These findings indicate that the initiation of self-fertilization predated the origin of the marmoratus-ocellatus clade. From mitochondrial DNA sequences and microsatellite data, we document a substantial genetic distance between Kryptolebias marmoratus and K. ocellatus, implying that the selfing capacity has persisted in these fishes for at least several hundred thousand years.

Strong population structure despite evidence of recent migration in a selfing hermaphroditic vertebrate, the mangrove killifish ( Kryptolebias marmoratus )

We employ a battery of 33 polymorphic microsatellite loci to describe geographical population structure of the mangrove killifish (Kryptolebias marmoratus), the only vertebrate species known to have a mixed‐mating system of selfing and outcrossing. Significant population genetic structure was detected at spatial scales ranging from tens to hundreds of kilometres in Florida, Belize, and the Bahamas. The wealth of genotypic information, coupled with the highly inbred nature of most killifish lineages due to predominant selfing, also permitted treatments of individual fish as units of analysis. Genetic clustering algorithms, neighbour‐joining trees, factorial correspondence, and related methods all earmarked particular killifish specimens as products of recent outcross events that could often be provisionally linked to specific migration events. Although mutation is the ultimate source of genetic diversity in K. marmoratus, our data indicate that interlocality dispersal and outcross‐mediated genetic recombination (and probably genetic drift also) play key proximate roles in the local ‘clonal’ dynamics of this species.