Andrey Tatarenkov

Andrey Tatarenkov
University of California, Irvine | UCI · Department of Ecology and Evolutionary Biology

Ph.D.

About

73
Publications
9,040
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
1,901
Citations

Publications

Publications (73)
Article
Introgression is a widespread evolutionary process leading to phylogenetic inconsistencies among distinct parts of the genomes, particularly between mitochondrial and nuclear-based phylogenetic reconstructions (e.g., mito-nuclear discordances). Here, we used mtDNA and genome-wide nuclear sites to provide the first phylogenomic-based hypothesis on t...
Article
Full-text available
Different mating systems are expected to affect the extent and direction of hybridization. Due to the different levels of sexual conflict, the weak inbreeder/strong outbreeder (WISO) hypothesis predicts that gametes from self-incompatible (SI) species should outcompete gametes from self-compatible (SC) ones. However, other factors such as timing of...
Article
Mangrove killifishes of the genus Kryptolebias have been historically classified as rare because of their small size and cryptic nature. Major gaps in distribution knowledge across mangrove areas, particularly in South America, challenge the understanding of the taxonomic status, biogeographical patterns and genetic structuring of the lineages comp...
Article
The disjunct distributions of freshwater organisms along coastal drainages are usually explained by palaeodrainages formed during sea‐level retreats that connected currently isolated basins, or by river capture from tectonic adjustments between adjoining watersheds. We evaluate the relative importance of these events on the genetic variation of fre...
Article
Different mating systems can strongly affect the extent of genetic diversity and population structure among species. Given the increased effects of genetic drift on reduced population size, theory predicts that species undergoing self-fertilisation should have greater population structure than outcrossed species; however, demographic dynamics may a...
Preprint
Full-text available
Different mating systems can strongly affect the extent of genetic diversity and population structure among species. Given the increased effects of genetic drift on reduced population size, theory predicts that species undergoing self-fertilization should have greater population structure than outcrossed species, however demographic dynamics may af...
Preprint
Full-text available
Hybridisation is a major source of evolutionary innovation. However, several prezygotic and postzygotic factors influence its likelihood and evolutionary outcomes. Differences in mating systems can have a major effect on the extent and direction of hybridisation and introgression. In plants, epigenetic mechanisms help to stabilize hybrid genomes an...
Article
Extreme inbreeding is expected to reduce the incidence of hybridization, serving as a prezygotic barrier. Mangrove rivulus is a small killifish that reproduces predominantly by self‐fertilization, producing highly homozygous lines throughout its geographic range. The Bahamas and Caribbean are inhabited by two highly diverged phylogeographic lineage...
Article
Full-text available
Sequential hermaphroditism (sex change) is understood to be a strategy that maximizes lifetime reproduction in systems where one sex confers highest fitness early in life, and the other later in life. This strategy is evolutionarily stable despite costs to growth, survival, or current reproduction. Few studies have examined advantages of sex change...
Article
Developmental stress from early life challenges impacts adult phenotype across a range of species. However, the potential transgenerational consequences for adult phenotype are largely unknown. Additionally, the possible impacts of natural hatch/birth order and natal brood composition in unmanipulated broods/litters on adult performance has been un...
Article
By definition, mating between individuals is infrequent in highly selfing organisms, and so too, therefore, hybridization should be rare between genetically divergent lineages in predominantly self-fertilizing species. Notwithstanding these expectations, here we report a remarkable case of natural hybridization between highly diverged phylogeograph...
Article
Full-text available
Fishes acclimated to hypoxic environments often increase gill surface area to improve O2uptake. In some species, surface area is increased via reduction of an interlamellar cell mass (ILCM) that fills water channels between gill lamellae. Amphibious fishes, however, may not increase gill surface area in hypoxic water because these species can inste...
Article
Full-text available
Annual killifish that are adapted to life in aquatic habitat that dries seasonally have evolved desiccation-resistant eggs capable of undergoing diapause, i.e. developmental arrest, at specific stages during embryology. Although noted for their remarkable ability to live at the land-water interface, species in the genus Rivulus are considered to be...
Article
The mangrove rivulus, Kryptolebias marmoratus, is one of only two self-fertilizing hermaphroditic fish and inhabits mangrove forests. While selfing can be advantageous, it reduces heterozygosity and decreases genetic diversity. Studies using microsatellites found that there are variable levels of selfing among populations of K. marmoratus but overa...
Article
Full-text available
Paleo-drainage connections and headwater stream-captures are two main historical processes shaping the distribution of strictly freshwater fishes. Recently, bathymetric-based methods of paleo-drainage reconstruction have opened new possibilities to investigate how these processes have shaped the genetic structure of freshwater organisms. In this co...
Data
Bayesian phylogenetic reconstructions for cytochrome b (cytB) and cytochrome oxidase I (coi) in Pareiorhaphis garbei, using HKY+I (cytB) and TrN+G (coi) as nucleotide substitution models. Pareiorhaphis cf. bahianus (MG496258 and MG496259) from Contas river basin (northeastern Brazil) was used as out-group. Posterior probabilities are shown above th...
Article
Full-text available
We use extensive geographical sampling and surveys of nuclear microsatellite and mitochondrial DNA loci to investigate the phylogeographic structure of the only recognized self-fertilizing vertebrates, the mangrove killifishes, currently thought to comprise two cryptic species, Kryptolebias marmoratus and Kryptolebias hermaphroditus. All genetic ma...
Article
The mangrove rivulus (Kryptolebias marmoratus) is one of two preferentially self-fertilizing hermaphroditic vertebrates. This mode of reproduction makes mangrove rivulus an important model for evolutionary and biomedical studies because long periods of self-fertilization result in naturally homozygous genotypes that can produce isogenic lineages wi...
Article
Full-text available
The complete mitochondrial genome was sequenced in a mangrove rivulus Kryptolebias marmoratus from western Florida using next-generation sequencing. The 17 329 bp-long genome was identical in length and 99.8% similar to a previously published genome of this species from a specimen of unknown geographic origin. Gene arrangement in K. marmoratus is s...
Article
Full-text available
Many vertebrate species have the ability to undergo weeks or even months of diapause (a temporary arrest of development during early ontogeny). Identification of diapause genes has been challenging due in part to the genetic heterogeneity of most vertebrate animals. Here we take the advantage of the mangrove rivulus fish (Kryptolebias marmoratus or...
Article
Full-text available
Kryptolebias marmoratus, a small killifish that lives in mangrove habitat from southern Florida to Brazil, is one of the planet's only known self-fertilizing hermaphroditic vertebrates. Generation after generation, hermaphroditic individuals simultaneously produce sperm and eggs and internally self-fertilize to produce what are, in effect, highly i...
Article
Full-text available
We present a Bayesian method for characterizing the mating system of populations reproducing through a mixture of self-fertilization and random outcrossing. Our method uses patterns of genetic variation across the genome as a basis for inference about reproduction under pure hermaphroditism, gynodioecy, and a model developed to describe the self-fe...
Article
The mangrove rivulus, Kryptolebias marmoratus (Rivulidae, Cyprinodontiformes), is phylogenetically embedded within a large clade of oviparous (egg laying) and otherwise mostly gonochoristic (separate sex) killifish species in the circumtropical suborder Aplocheiloidei. It is unique in its reproductive mode: K. marmoratus is essentially the world's...
Preprint
Full-text available
We present a Bayesian method for characterizing the mating system of populations reproducing through a mixture of self-fertilization and random outcrossing. Our method uses patterns of genetic variation across the genome as a basis for inference about pure hermaphroditism, androdioecy, and gynodioecy. We extend the standard coalescence model to acc...
Article
Full-text available
We used 32 polymorphic microsatellite loci to investigate how a mixed-mating system affects population genetic structure in Central American populations (N = 243 individuals) of the killifish Kryptolebias marmoratus (mangrove rivulus), 1 of 2 of the world's only known self-fertilizing vertebrates. Results were also compared with previous microsatel...
Article
We present a Bayesian method for characterizing the mating system of populations reproducing through a mixture of self-fertilization and random outcrossing. Our method uses patterns of genetic variation across the genome as a basis for inference about pure hermaphroditism, androdioecy, and gynodioecy. We extend the standard coalescence model to acc...
Article
Full-text available
For more than two decades, mitochondrial DNA sequences and simple sequence repeats (SSRs, or microsatellite loci) have served as gold standards in population genetics. More recently, next generation sequencing (NGS) has enabled researchers to address biological questions that can benefit from hundreds or even thousands of nuclear single-nucleotide...
Article
Full-text available
Population density might be an important variable in determining the degree of multiple paternity. In a previous study, a high level of multiple paternity was detected in the shiner perch Cymatogaster aggregata, a species with high population density and a high mate encounter rate. The tule perch Hysterocarpus traski is phylogenetically closely rel...
Article
Full-text available
Fertilization assurance (Baker's contention) and multilocus coadaptation (Allard's argument) are two distinct hypotheses for the adaptive significance of self-fertilization in hermaphroditic taxa, and both scenarios have been invoked to rationalize isogenicity via incest in various plants and invertebrate animals with predominant selfing. Here we c...
Article
Full-text available
The mangrove rivulus Kryptolebias marmoratus and a closely related species are the world's only vertebrates that routinely self-fertilize. Such uniqueness presents a model for understanding why this reproductive mode, common in plants and invertebrates, is so rare in vertebrates. A survey of 32 highly polymorphic loci in >200 specimens of mangrove...
Article
This study documents unexpectedly low levels of intra and interpopulation genetic diversity in Kryptolebias ocellatus, an androdioecious and predominantly self-fertilizing killifish from south-eastern Brazil. This finding generally is inconsistent with the established opinion that the K. ocellatus and K. marmoratus clade originated in this geograph...
Article
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...
Article
Full-text available
We summarize the genetic literature on polygamy rates and sire numbers per clutch in invertebrate animals that brood their offspring and then compare findings with analogous data previously compiled for vertebrate species displaying viviparity or other pregnancy-like syndromes. As deduced from molecular parentage analyses of several thousand broods...
Data
Microsatellite genotypes of 164 individuals from 42 laboratory stocks representing 21 lines of Kryptolebias marmoratus. (0.09 MB XLS)
Data
Full-text available
Positions of some laboratory lines in a larger mtDNA tree. Additional samples used in this tree are those from [21]. Laboratory lines are highlighted in yellow. Lines PanRS (Panama) and Gitmo (Cuba) cluster with Kryptolebias ocellatus. (0.08 MB PDF)
Data
Full-text available
Microsatellite-based neighbor-joining tree showing positions of 22 individuals representing 21 lines (line Dan06 represented by 2 individuals) among fish specimens collected in nature (using datasets from [20], [21]). Laboratory lines are shown in red. (0.04 MB PDF)
Data
Summary of samples removed based upon genotype. (0.02 MB XLS)
Article
Full-text available
The hermaphroditic Mangrove Killifish, Kryptolebias marmoratus, is the world's 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 ve...
Article
Swordtails (Xiphophorus; Poeciliidae) have figured prominently in research on fish mating behaviours, sexual selection, and carcinogenesis, but their population structures and dispersal patterns have been relatively neglected. Using nine microsatellite loci, we estimated genetic differentiation in Xiphophorus helleri within and between adjacent str...
Article
Full-text available
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 eviden...
Article
For many species in nature, a sire's 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 a...
Article
The population genetic structure of marine species lacking free-swimming larvae is expected to be strongly affected by random genetic drift among populations, resulting in genetic isolation by geographical distance. At the same time, ecological separation over microhabitats followed by direct selection on those parts of the genome that affect adapt...
Article
The marine snail Littorina mariae Sacchi & Rastelli occurs in high numbers in the littoral zone on fucoid macro-algae. The eggs are laid on the seaweed and d e velopment to miniature snails takes place without any pelagic larval stage. We have mapped the genetic variation of 30 enzyme loci in populations from eight small islands within 15 km of eac...
Article
Full-text available
We studied nucleotide sequence variation at the gene coding for dopa decarboxylase (Ddc) in seven populations of Drosophila melanogaster. Strength and pattern of linkage disequilibrium are somewhat distinct in the extensively sampled Spanish and Raleigh populations. In the Spanish population, a few sites are in strong positive association, whereas...
Article
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...
Article
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...
Article
Full-text available
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 killifis...
Article
Full-text available
Behavioral observations have suggested that Channel Catfish, Ictalurus Pundatus, spawn as monogamous pairs and that males alone provide subsequent care to the resulting embryos and fry. However, genetic monogamy is quite uncommon in fish and is not necessarily correctly predicted by apparent social interactions. Here we develop and employ seven mic...
Article
Full-text available
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 ana...
Article
We describe DNA sequence polymorphisms at six loci (Acp26Aa, Acp26Ab, Acp29AB, Idgf1, Idgf3 and Ddc), all on the second chromosome of Drosophila melanogaster in one natural European population. Previous studies considering these loci separately showed that some of them were affected by natural selection. However, demographic processes or population...
Article
Full-text available
The mangrove killifish (Kryptolebias marmoratus) is the only vertebrate known to be capable of self-fertilization. Its gonad is typically an ovotestis that simultaneously produces eggs and sperm, and fertilization is internal. Although most populations of this species consist primarily or exclusively of hermaphroditic individuals, gonochoristic mal...
Article
Brown seaweeds of the genus Fucus occupy a wide variety of temperate coastal habitats. The genus is evolutionary dynamic with recent radiations to form morphologically distinct taxa. In the brackish Baltic Sea, fucoids are the only perennial canopy-forming macroalgae. The most northern populations of Fucus occur permanently submerged in extremely l...
Article
Reproduction of attached large brown algae is known to occur only by sexual zygotes. Using microsatellites we show evolution of asexual reproduction in the bladder wrack promoting population persistence in the brackish water Baltic Sea (< 6 psu). Here a dwarf morph of Fucus vesiculosus is dominated by a single clone but clonal reproduction is also...
Article
Full-text available
We survey DNA sequence polymorphisms at the Sod locus and four neighboring regions of Drosophila melanogaster, spanning 55,513 base pairs (bp), in 15 strains from a natural population, plus one reference laboratory strain and one strain of Drosophila simulans. Our objective is to characterize a proposed selective sweep that occurred at a locus clos...
Article
Earlier studies of Swedish populations of the marine snail Littorina fabalis show that snails from different microhabitats (with a greater and lesser exposure to wave action) have almost diagnostic differences in one allozyme locus (arginine kinase, Ark), and differ in adult size. Snails with 'sheltered' and 'exposed' Ark genotypes occur in sympatr...
Article
Cs, a gene with unknown function, and amd and Ddc, which encode decarboxylases, are among the most closely spaced genes in D. melanogaster. Untranslated 3' ends of the convergently transcribed genes Cs and Ddc are known to overlap by 88bp. A number of questions arise about the organization of this tightly-packed gene region and about the evolution...
Article
Full-text available
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...
Article
Studies of allozyme variation may reveal unexpected patterns of genetic variation which challenge earlier conclusions of species delimitations based on morphological data. However, allozyme variation alone may not be sufficient to resolve this kind of problem. For example, populations of the marine intertidal snail Littorina fabalis (=Littorina mar...
Article
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-specifi...
Article
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 microhabital-specific variation may contribute to the total differentiation. To appreciate the relative contributions of geographic variation and habitat-specifi...
Article
The proposed software allows calculation of Nei's coefficients of genetic distance and genetic identity from allele frequencies; estimation of their standard error by asymptotic formulae; and estimation of confidence intervals based on standard error, as well as bootstrapped confidence intervals. The C programming language is used. The program (lis...
Article
Genetic comparison of two sibling species of marine gastropods, Littorina marine Sacchi and Rastelli and L. obtusata (L.), was conducted using electrophoresis of proteins encoded by 29 loci. Three loci were fixed for different alleles, and in eight polymorphic loci allele frequencies differed in sympatric samples. This supports earlier findings tha...
Article
Genetic differentiation among eight samples of Littorina brevicula from Peter the Great Bay was estimated using five highly polymorphic loci as genetic markers. The coefficient of relative genetic-differentiation was low (G(ST) = 1.6%). This is probably caused by intense gene flow be tween snail settlements because L. brevicula has a planktonic lar...
Article
The marine snail Litton'na mariae Sacchi & Rastelli occurs in high numbers in the littoral zone on fucoid macro-algae. The eggs are laid on the seaweed and development to miniature snails takes place without any pelagic larval stage. We have mapped the genetic variation of 30 enzyme loci in populations from eight small islands within 15 km of each...