Evolutionary Genetic Studies Research Articles

Characterization of 24 microsatellite markers in 11 species of fire ants in the genus Solenopsis (Hymenoptera: Formicidae)

The social parasite ant Solenopsis daguerrei infests colonies of several mound-building fire ant species. Twenty-four microsatellite markers were isolated from a repeat-enriched genomic library of S. daguerrei. Eleven loci were polymorphic in this ant with two to six alleles per locus. Expected heterozygosity ranged from 0.0222 to 0.7940 among loci. Most microsatellites amplified successfully across the 11 Solenopsis species tested and will be useful for evolutionary genetic studies in this diverse ant group.

Weeds of change: Cardamine hirsuta as a new model system for studying dissected leaf development

Cardamine hirsuta, a small crucifer closely related to the model organism Arabidopsis thaliana, offers high genetic tractability and has emerged as a powerful system for studying the genetic basis for diversification of plant form. Contrary to A. thaliana, which has simple leaves, C. hirsuta produces dissected leaves divided into individual units called leaflets. Leaflet formation requires activity of Class I KNOTTED1-like homeodomain (KNOX) proteins, which also promote function of the shoot apical meristem (SAM). In C. hirsuta, KNOX genes are expressed in the leaves whereas in A. thaliana their expression is confined to the SAM, and differences in expression arise through cis-regulatory divergence of KNOX regulation. KNOX activity in C. hirsuta leaves delays the transition from proliferative growth to differentiation thus facilitating the generation of lateral growth axes that give rise to leaflets. These axes reflect the sequential generation of cell division foci across the leaf proximodistal axis in response to auxin activity maxima, which are generated by the PINFORMED1 (PIN1) auxin efflux carriers in a process that resembles organogenesis at the SAM. Delimitation of C. hirsuta leaflets also requires the activity of CUP SHAPED COTYLEDON (CUC) genes, which direct formation of organ boundaries at the SAM. These observations show how species-specific deployment of fundamental shoot development networks may have sculpted simple versus dissected leaf forms. These studies also illustrate how extending developmental genetic studies to morphologically divergent relatives of model organisms can greatly help elucidate the mechanisms underlying the evolution of form.

Species-Wide Genetic Variation and Demographic History of Drosophila sechellia, a Species Lacking Population Structure

Long-term persistence of species characterized by a reduced effective population size is still a matter of debate that would benefit from the description of new relevant biological models. The island endemic specialist Drosophila sechellia has received considerable attention in evolutionary genetic studies. On the basis of the analysis of a limited number of strains, a handful of studies have reported a strikingly depleted level of genetic variation but little is known about its demographic history. We extended analyses of nucleotide polymorphism in D. sechellia to a species-wide level using 10 nuclear genes sequenced in 10 populations. We confirmed that D. sechellia exhibits little nucleotide-sequence variation. It is characterized by a low effective population size, >10-fold lower than that of D. simulans, which ranks D. sechellia as the least genetically diverse Drosophila species. No obvious population subdivision was detected despite its fragmented geographic distribution on different islands. We used approximate Bayesian computation (ABC) to test for demographic scenarios compatible with the geological history of the Seychelles and the ecology of D. sechellia. We found that while bottlenecks cannot account for the pattern of molecular evolution observed in this species, scenarios close to the null hypothesis of a constant population size are well supported. We discuss these findings with regard to adaptive features specific to D. sechellia and its life-history strategy.

STUDIES ON CLONAL DIVERSITY OF GIBEL CARP, <I>CARASSIUS AURATUS GIBELIO</I>, FROM THE IRTYSH RIVER WATER SYSTEM IN XINJIANG PROVINCE

Gibel carp, Carassius auratus gibelio Bloch, as a subspecies of Carassius auratus, has a wide geographic distribution from northern Europe to Asia. As a new culture target, it has been used widely for aquaculture practice in recent 30 years in China, and its production capacity has increased up to 2 billion kilograms annually. Gibel carp possess several interesting characteristics: 1) It is a triploid fish with more than 150 chromosomes, 2) It exists as a bisexual population with predominantly more females (an 80 : 20 female: male ratio) in natural habitats, 3) It has dual reproductive modes of gynogenesis and bisexual reproduction, 4) Various gynogenetic clones have been identified. These features make gibel carp a promising study model for evolutionary genetics, developmental biology and selective breeding. Recently, we have detected clonal diversity of gibel carp in Fangzheng stock hatchery of Heilongjiang Province and Qihe stock hatchery of Henan Province. Up to now, however, little information had been known about the status of gibel carp populations from the Irtysh River water system in Xinjiang Province. In order to obtain a better understanding of the status of clonal diversity of the gibel carp populations, four populations of Carassius auratus were collected from the Irtysh River water system in this study. Flow cytometry was applied to analyze their blood cells, revealing that all of them were triploid gibel carp. Then, a total of eight different clones were clearly discriminated from these gibel carp populations by analysis of serum transferrin phenotypes. Among them, four clones were identical to those identified previously, whereas, the other four were new. Clones A and M were the most wide-ranging, occurring in all of the four populations. Clone J appeared in two populations. Each of the other five clones was specific to single population. These distribution patterns of different clones within populations might reflect clones being able to migrate and differences in viability of a clone among different water bodies. Among these sampled populations of gibel carp, one had the level of clonal diversity obviously lower than those in the other tree, similar to those in populations reported, probably suggesting negative effects of human activities such as hydraulic engineering construction and overharvesting. The clonal diversity revealed in this study will likely benefit evolutionary genetics and selective breeding studies. At the same time, this work also highlights the significance of protecting clonal diversity Of gibel carp in the Irtysh River water system.

Development and characterization of 10 polymorphic tetranucleotide microsatellite markers for New Mexico spadefoot toads (Spea multiplicata)

Ten tetranucleotide loci were isolated from a New Mexico spadefoot toad (Spea multiplicata) microsatellite-enriched genomic library. To assess the degree of variability in these loci, we genotyped 120 S. multiplicata tadpoles collected from six playa wetlands in the Southern High Plains. Loci revealed a high degree of allelic diversity (4–20 alleles), observed heterozygosity (0.466–0.806), and expected heterozygosity (0.485–0.900). With the isolation and characterization of these microsatellite loci there now exists 19 microsatellite loci for S. multiplicata that will prove to be powerful molecular tools for ecological, evolutionary, and conservation genetic studies on New Mexico and Plains (S. bombifrons) spadefoot toads.

Embryogenesis and laboratory maintenance of the foam‐nesting túngara frogs, genus Engystomops (= Physalaemus)

The vast majority of embryological research on amphibians focuses on just a single genus of frogs, Xenopus. To attain a more comprehensive understanding of amphibian development, experimentation on non-model frogs will be essential. Here, we report on the early development, rearing, and embryological analysis of túngara frogs (genus Engystomops, also called Physalaemus). The frogs Engystomops pustulosus, Engystomops coloradorum, and Engystomops randi construct floating foam-nests with small eggs. We define a table of 23 stages for the developmental period in the foam-nest. Embryos were immunostained against Lim1, neural, and somite-specific proteins and the expression pattern of RetinoBlastoma Binding Protein 6 (RBBP6) was analyzed by in situ hybridization. Due to their brief life-cycle, frogs belonging to the genus Engystomops are attractive for comparative and genetic studies of development. Developmental Dynamics 238:1444-1454, 2009. (c) 2009 Wiley-Liss, Inc.

Haplotyping Methods for Pedigrees

Haplotypes provide valuable information in the study of diseases, complex traits, population histories, and evolutionary genetics. With the dramatic increase in the number of available single nucleotide polymorphism (SNP) markers, haplotype inference (haplotyping) using observed genotype data has become an important component of genetic studies in general and of statistical gene mapping in particular. Existing haplotyping methods include (1) population-based methods, (2) methods for pooled DNA samples, and (3) methods for family and pedigree data. The methods and computer programs for population data and pooled DNA samples were reviewed recently in the literature. As several authors noted, family and pedigree datasets are abundant and have unique advantages. In the past twenty years, many haplotyping methods for family and pedigree data have been developed. Therefore, in this contribution we review haplotyping methods and the corresponding computer programs suitable for family and pedigree data and discuss their applications and limitations. We explore the connections among these methods, and describe the challenges that remain to be addressed.

Astyanax mexicanus, the Blind Mexican Cave Fish: A Model for Studies in Development and Morphology: Figure 1.

INTRODUCTIONThe perpetual darkness of caves has two important consequences for permanent inhabitants. First, eyes and pigmentation lose their primary functions. Second, in the absence of photosynthesis, food is rare. For these reasons, cave-adapted species typically have reduced eyes and pigmentation and increased or more efficient metabolisms. Additionally, other senses are usually augmented to compensate for the loss of vision. Identifying the genetic bases underlying these phenotypic changes will enhance our understanding of the specific pathways involved in control of these phenotypes and, in general, the evolutionary process. Unfortunately, the genetics of most cave animals cannot be studied because they are not easily bred. Blind Mexican tetras, Astyanax mexicanus, are the valuable exception to this rule because fish from the various cave populations are fully interfertile with one another and with eyed sister forms still living in nearby surface streams. Hybrids between surface and cave forms permit genetic analysis of their differences, and study of the pure forms as well as of hybrids allows study of their developmental differences. Quantitative trait loci (QTL) analysis has already identified some specific genes responsible for differences between cave and surface forms as well as other likely candidates; more will be added in the future. This system is a valuable addition to the array of existing models for the study of developmental and evolutionary genetics because cave populations are repositories of numerous naturally occurring mutations affecting development of the eyes and other senses, pigmentation, bone structure, metamerism, and metabolism. These alleles have been prescreened by natural selection for high viability, which simplifies their study. In contrast, new alleles obtained through mutagenesis in other model species are typically burdened with lower viability.

Maximum-Likelihood Estimation of Site-Specific Mutation Rates in Human Mitochondrial DNA From Partial Phylogenetic Classification

The mitochondrial DNA hypervariable segment I (HVS-I) is widely used in studies of human evolutionary genetics, and therefore accurate estimates of mutation rates among nucleotide sites in this region are essential. We have developed a novel maximum-likelihood methodology for estimating site-specific mutation rates from partial phylogenetic information, such as haplogroup association. The resulting estimation problem is a generalized linear model, with a nonstandard link function. We develop inference and bias correction tools for our estimates and a hypothesis-testing approach for site independence. We demonstrate our methodology using 16,609 HVS-I samples from the Genographic Project. Our results suggest that mutation rates among nucleotide sites in HVS-I are highly variable. The 16,400-16,500 region exhibits significantly lower rates compared to other regions, suggesting potential functional constraints. Several loci identified in the literature as possible termination-associated sequences (TAS) do not yield statistically slower rates than the rest of HVS-I, casting doubt on their functional importance. Our tests do not reject the null hypothesis of independent mutation rates among nucleotide sites, supporting the use of site-independence assumption for analyzing HVS-I. Potential extensions of our methodology include its application to estimation of mutation rates in other genetic regions, like Y chromosome short tandem repeats.

Medaka genome project

The medaka Oryzias latipes is a small egg-laying freshwater teleost, and has become an excellent model system for ecotoxicology, developmental genetics, genomics and evolutionary biology studies. A high-quality draft genome sequence (700 Mb) of the medaka inbred strain, Hd-rR, has now been completed. In this review, we present an overview of the medaka genome project and describe the substantial genomic resources and genome browsers through which researchers can now freely access these resources. We also present specific findings that have been obtained using these tools, such as sex chromosome differentiation, gene prediction and gene evolution.

A highly polymorphic insertion in the Y-chromosome amelogenin gene can be used for evolutionary biology, population genetics and sexing in Cetacea and Artiodactyla

BackgroundThe early radiation of the Cetartiodactyla is complex, and unambiguous molecular characters are needed to clarify the positions of hippotamuses, camels and pigs relative to the remaining taxa (Cetacea and Ruminantia). There is also a need for informative genealogic markers for Y-chromosome population genetics as well as a sexing method applicable to all species from this group. We therefore studied the sequence variation of a partial sequence of the evolutionary conserved amelogenin gene to assess its potential use in each of these fields.Results and discussionWe report a large interstitial insertion in the Y amelogenin locus in most of the Cetartiodactyla lineages (cetaceans and ruminants). This sex-linked size polymorphism is the result of a 460–465 bp inserted element in intron 4 of the amelogenin gene of Ruminants and Cetaceans. Therefore, this polymorphism can easily be used in a sexing assay for these species.When taking into account this shared character in addition to nucleotide sequence, gene genealogy follows sex-chromosome divergence in Cetartiodactyla whereas it is more congruent with zoological history when ignoring these characters. This could be related to a loss of homology between chromosomal copies given the old age of the insertion.The 1 kbp Amel-Y amplified fragment is also characterized by high nucleotide diversity (64 polymorphic sites spanning over 1 kbp in seven haplotypes) which is greater than for other Y-chromosome sequence markers studied so far but less than the mitochondrial control region.ConclusionThe gender-dependent polymorphism we have identified is relevant not only for phylogenic inference within the Cetartiodactyla but also for Y-chromosome based population genetics and gender determination in cetaceans and ruminants. One single protocol can therefore be used for studies in population and evolutionary genetics, reproductive biotechnologies, and forensic science.

Embryology of Ceratopteris richardii (Pteridaceae, tribe Ceratopterideae), with emphasis on placental development

This comprehensive study of early embryology in Ceratopteris richardii combines light microscopy with the first ultrastructural evaluation of any pteridophyte embryo. Emphasis is placed on ontogeny of the foot and placental transfer cells. The embryology of C. richardii shares many similarities with that of other polypodiacious ferns while exhibiting distinctive division patterns. Formative embryonic stages have been reconstructed into three-dimensional models for ease of interpretation. The zygote divides perpendicular to the gametophyte plane and anterioposterior axis. This division establishes a prone embryological habit that maximizes rapid independent establishment of a leaf-root axis in a cordate gametophyte. After the formation of a globular eight-celled stage, initials of the first leaf, and root and shoot apical meristems are defined early by discrete formative divisions. Concomitantly, the foot expands and differentiates to transport nutrients from the gametophyte for the developing embryonic organs. Transfer cell wall ingrowth deposition begins in the gametophyte placental cells before the adjacent sporophyte cells just after the eight-celled stage. These observations provide an anatomical framework for future comparative developmental genetic studies of embryogenesis in free-sporing plants.

Fishing lines, time‐delayed guideposts, and other tricks used by developing pharyngeal neurons in Caenorhabditis elegans

The 20 neurons that innervate the Caenorhabditis elegans pharynx form a simple nervous system that develops and operates in near complete isolation from the rest of the worm body and, therefore, offers a manageable degree of complexity for developmental genetics studies. This review discusses the progress that has been made in determining the mechanisms by which 4 of the 20 pharyngeal neurons develop, and emphasizes surprising processes that add to the classic growth cone guidance model which is usually thought to explain how most axons establish their trajectories.

Development of 17 microsatellite markers for Ceratosolen constrictus, the pollinating fig wasp of Ficus fistulosa

The obligate mutualism between figs (Ficus) and fig pollinating wasps (Agaonidae) is regarded as a classic example of mutualism. Seventeen polymorphic microsatellite loci were developed for Ceratosolen constrictus, the pollinating wasp of the dioecious fig Ficus fistulosa. The number of alleles per locus ranged from two to 15 and the observed and expected heterozygosities ranged from 0.040 to 0.846 and from 0.040 to 0.916, respectively. These microsatellite loci offer a powerful tool for evolutionary and population genetic studies in C. constrictus, and gene flow of F. fistulosa.

Change of Genetic Determinants of Left Ventricular Structure in Adolescence: Longitudinal Evidence From the Georgia Cardiovascular Twin Study

Genetic contribution to left ventricular (LV) structure is generally recognized, but whether and how this influence varies by ethnicity or with age is unknown. Participants were 517 European-American (EA) and African-American (AA) twin pairs (mean age: 14.6 +/- 3.0) at visit 1 and 422 EA and AA twin pairs at follow-up 4.1 years later. Echocardiograms were obtained on both visits. Data were analyzed using the structural equation modeling software Mx. Body mass index (BMI) was a strong predictor for all LV measures at both visits 1 and 2, accounting for 3.5-24.2% of the total variance. Hemodynamics explained up to 4.5% additional LV measures variance. After adjusting for BMI, LV measures showed substantial heritability (range: 21-71%). Best-fitting longitudinal models revealed considerable novel genetic effects on the interventricular septum, posterior wall-, and relative wall thickness (RWT) (but not LV internal diameter), accounting for 32-41% of the phenotypic variance at visit 2, with no significant gender and ethnic effects. There was a gender difference for LV mass index in AAs (P < 0.01), with a significant influence of novel genetic effects in males (47%), but not in females. No gender difference was seen in EAs, with 34% of the phenotypic variance at visit 2 attributable to novel genetic effects. The heritability of cardiac structure and geometry was equally substantial in both AAs and EAs. Significant novel genetic influences were detected for all measures but LV inner diameter and LV mass index in AA females. Further developmental genetic studies are warranted to elucidate the nature of the emerging gene effects during the transition from adolescence to adulthood.

Microsatellites: A tool for evolutionary genetic studies of western Palearctic water frogs

Genotypic variation at six of 67 microsatellite loci we developed from Rana ridibunda, containing di- or trinucleotide simplesequence repeats, confirms the value of microsatellites as an evolutionary genetic tool for studying western Palearctic water frogs, a model system characterized by clonal reproduction in natural hybrid lineages. R. ridibunda, Rana lessonae. and their hemiclonal hybrid Rana esculenta, which transmits only its ridibunda genome to gametes, are highly variable in central Poland and northern Switzerland: with one exception (a locus that is part of a coding region), each locus was polymorphic in each taxon when scorable, and the number of alleles was high (in Swiss lessonae-esculenta populations, 1-6 per locus, total 13, for ridibunda genomes; 1-9 per locus, total 23, for lessonae genomes; 3 shared by both genomes). Estimated repeat numbers ranged from 3 to 14 for trinucleotide- and from 6 to 27 for dinucleotide-repeats. Nonamplifying (null) alleles, problematic because they underestimate genotypic variability if undetected, occur in ridibunda genomes of Swiss R. esculenta at one locus: apparent lessonae null alleles at another locus were subsequently resolved for several segregating alleles evidenced by bands of much lower intensity. Two loci had multiple ridibunda alleles in Swiss R. esculenta and thus discriminate between hemiclones. with a resolution superior to that of allozymes. Adding these two loci to our protein electrophoretic data (7 loci) more than doubled the number of hemiclones detected, showed that several allozyme-defined hemiclones are composites of multiple microsatellite hemiclones, and revealed clonal diversity in populations that are uniclonal by allozyme data. The extent to which microsatellite-defined hemiclones result from primary hybridizations or from subsequent mutations in ridibunda genomes of R. esculenta lineages remains to be determined. A sample of newly metamorphosed R. ridibunda from hybrid × hybrid matings collected at a Swiss population in the fall had a significant heterozygote excess at the two loci that varied in ridibunda genomes; this shows that most, probably all, of them originated from inter- rather than intrahemiclonal matings, in accord with the idea that the usual hybrid × hybrid inviability in lessonae-esculenta systems is caused by deleterious recessive alleles on the clonally inherited ridibunda genomes. Three of four microsatellite loci tested amplified in most species of western Palearctic water frogs.

Bayesian approaches in evolutionary quantitative genetics

The study of evolutionary quantitative genetics has been advanced by the use of methods developed in animal and plant breeding. These methods have proved to be very useful, but they have some shortcomings when used in the study of wild populations and evolutionary questions. Problems arise from the small size of data sets typical of evolutionary studies, and the additional complexity of the questions asked by evolutionary biologists. Here, we advocate the use of Bayesian methods to overcome these and related problems. Bayesian methods naturally allow errors in parameter estimates to propagate through a model and can also be written as a graphical model, giving them an inherent flexibility. As packages for fitting Bayesian animal models are developed, we expect the application of Bayesian methods to evolutionary quantitative genetics to grow, particularly as genomic information becomes more and more associated with environmental data.

Bird-pollinated flowers in an evolutionary and molecular context

Evolutionary shifts to bird pollination (ornithophily) have occurred independently in many lineages of flowering plants. This shift affects many floral features, particularly those responsible for the attraction of birds, deterrence of illegitimate flower visitors (particularly bees), protection from vigorous foraging by birds, and accurate placement of pollen on bird's bodies. Red coloration appears to play a major role in both bee-deterrence and bird-attraction. Other mechanisms of bird-attraction include the production of abundant dilute nectar and the provision of secondary perches (for non-hovering birds). As a result of selection for similar phenotypic traits in unrelated bird-pollinated species, a floral syndrome of ornithophily can be recognized, and this review surveys the component floral traits. The strong convergent evolution evident in bird-pollinated flowers raises a question about the nature of the genetic mechanisms underlying such transitions and whether the same gene systems are involved in most cases. As yet there is too little information to answer this question. However, some promising model systems have been developed that include closely related bee and bird-pollinated flowers, such as Ipomoea, Mimulus, and Lotus. Recent studies of floral developmental genetics have identified numerous genes important in the development of the floral phenotype, which are also potential candidates for involvement in shifts between bee-pollination and bird pollination. As more whole-genome information becomes available, progress should be rapid.

Detecting polymorphic regions in Arabidopsis thaliana with resequencing microarrays

Whole-genome oligonucleotide resequencing arrays have allowed the comprehensive discovery of single nucleotide polymorphisms (SNPs) in eukaryotic genomes of moderate to large size. With this technology, the detection rate for isolated SNPs is typically high. However, it is greatly reduced when other polymorphisms are located near a SNP as multiple mismatches inhibit hybridization to arrayed oligonucleotides. Contiguous tracts of suppressed hybridization therefore typify polymorphic regions (PRs) such as clusters of SNPs or deletions. We developed a machine learning method, designated margin-based prediction of polymorphic regions (mPPR), to predict PRs from resequencing array data. Conceptually similar to hidden Markov models, the method is trained with discriminative learning techniques related to support vector machines, and accurately identifies even very short polymorphic tracts (<10 bp). We applied this method to resequencing array data previously generated for the euchromatic genomes of 20 strains (accessions) of the best-characterized plant, Arabidopsis thaliana. Nonredundantly, 27% of the genome was included within the boundaries of PRs predicted at high specificity ( approximately 97%). The resulting data set provides a fine-scale view of polymorphic sequences in A. thaliana; patterns of polymorphism not apparent in SNP data were readily detected, especially for noncoding regions. Our predictions provide a valuable resource for evolutionary genetic and functional studies in A. thaliana, and our method is applicable to similar data sets in other species. More broadly, our computational approach can be applied to other segmentation tasks related to the analysis of genomic variation.

Understanding of bat wing evolution takes flight

It has long been debated whether the processes and mechanisms responsible for phenotypic variation within a population or between closely related populations can be extrapolated to explain evolutionary trends over longer phylogenetic distances and especially the generation of novel structures. Although there has been great progress in recent years in addressing the genetic basis for microevolutionary changes, for the most part these efforts have done little to address this debate. Evolutionary genetic studies, by their nature, can only be applied to closely related groups. For example, quantitative trait mapping is limited to species with distinct morphological traits that are capable of producing viable progeny when crossed either naturally or artificially. There are only a few cases in which linkage mapping has thus far been applied even at the distance of interspecific hybrids to identify loci responsible for morphological differences between highly related species (Sucena et al. 2003; Shapiro et al. 2004; Colosimo et al. 2005; Kronforst et al. 2006; Protas et al. 2006; McGregor et al. 2007). While the genomes of more distantly related taxa can be compared, the effect of molecular drift over millions of years has generated a large noise of sequence variation that makes the identification of specific and functionally relevant changes analogous to finding a needle in a haystack. In this issue of Genes & Development, Cretekos et al. (2008) have found one such needle—an enhancer of the paired-box homeodomain transcription factor, Prx1, that accounts for at least part of the extension of the long bones in the wings of bats.