Admixture and Genetic Diversity Distribution Patterns of Non-Recombining Lineages of Native American Ancestry in Colombian Populations

Genetic diversity of present American populations results from very complex demographic events involving different types and degrees of admixture. Through the analysis of lineage markers such as mtDNA and Y chromosome it is possible to recover the original Native American haplotypes, which remained identical since the admixture events due to the absence of recombination. However, the decrease in the effective population sizes and the consequent genetic drift effects suffered by these populations during the European colonization resulted in the loss or under-representation of a substantial fraction of the Native American lineages. In this study, we aim to clarify how the diversity and distribution of uniparental lineages vary with the different demographic characteristics (size, degree of isolation) and the different levels of admixture of extant Native groups in Colombia. We present new data resulting from the analyses of mtDNA whole control region, Y chromosome SNP haplogroups and STR haplotypes, and autosomal ancestry informative insertion-deletion polymorphisms in Colombian individuals from different ethnic and linguistic groups. The results demonstrate that populations presenting a high proportion of non-Native American ancestry have preserved nevertheless a substantial diversity of Native American lineages, for both mtDNA and Y chromosome. We suggest that, by maintaining the effective population sizes high, admixture allowed for a decrease in the effects of genetic drift due to Native population size reduction and thus resulting in an effective preservation of the Native American non-recombining lineages.     

Episodes of Diversification and Isolation in Island Southeast Asian and Near Oceanian Male Lineages

Island Southeast Asia (ISEA) and Oceania host one of the world’s richest assemblages of human phenotypic, linguistic, and cultural diversity. Despite this, the region’s male genetic lineages are globally among the last to remain unresolved. We compiled ∼9.7 Mb of Y chromosome (chrY) sequence from a diverse sample of over 380 men from this region, including 152 first reported here. The granularity of this data set allows us to fully resolve and date the regional chrY phylogeny. This new high-resolution tree confirms two main population bursts: multiple rapid diversifications following the region’s initial settlement ∼50 kya, and extensive expansions <6 kya. Notably, ∼40–25 kya the deep rooting local lineages of C-M130, M-P256, and S-B254 show almost no further branching events in ISEA, New Guinea, and Australia, matching a similar pause in diversification seen in maternal mitochondrial DNA lineages. The main local lineages start diversifying ∼25 kya, at the time of the last glacial maximum. This improved chrY topology highlights localized events with important historical implications, including pre-Holocene contact between Mainland and ISEA, potential interactions between Australia and the Papuan world, and a sustained period of diversification following the flooding of the ancient Sunda and Sahul continents as the insular landscape observed today formed. The high-resolution phylogeny of the chrY presented here thus enables a detailed exploration of past isolation, interaction, and change in one of the world’s least understood regions.     

Demographic Inference Reveals African and European Admixture in the North American Drosophila melanogaster Population

Drosophila melanogaster spread from sub-Saharan Africa to the rest of the world colonizing new environments. Here, we modeled the joint demography of African (Zimbabwe), European (The Netherlands), and North American (North Carolina) populations using an approximate Bayesian computation (ABC) approach. By testing different models (including scenarios with continuous migration), we found that admixture between Africa and Europe most likely generated the North American population, with an estimated proportion of African ancestry of 15%. We also revisited the demography of the ancestral population (Africa) and found—in contrast to previous work—that a bottleneck fits the history of the population of Zimbabwe better than expansion. Finally, we compared the site-frequency spectrum of the ancestral population to analytical predictions under the estimated bottleneck model.     

Identification of Genetic Variation on the Horse Y Chromosome and the Tracing of Male Founder Lineages in Modern Breeds

The paternally inherited Y chromosome displays the population genetic history of males. While modern domestic horses (Equus caballus) exhibit abundant diversity within maternally inherited mitochondrial DNA, no significant Y-chromosomal sequence diversity has been detected. We used high throughput sequencing technology to identify the first polymorphic Y-chromosomal markers useful for tracing paternal lines. The nucleotide variability of the modern horse Y chromosome is extremely low, resulting in six haplotypes (HT), all clearly distinct from the Przewalski horse (E. przewalskii). The most widespread HT1 is ancestral and the other five haplotypes apparently arose on the background of HT1 by mutation or gene conversion after domestication. Two haplotypes (HT2 and HT3) are widely distributed at high frequencies among modern European horse breeds. Using pedigree information, we trace the distribution of Y-haplotype diversity to particular founders. The mutation leading to HT3 occurred in the germline of the famous English Thoroughbred stallion “Eclipse” or his son or grandson and its prevalence demonstrates the influence of this popular paternal line on modern sport horse breeds. The pervasive introgression of Thoroughbred stallions during the last 200 years to refine autochthonous breeds has strongly affected the distribution of Y-chromosomal variation in modern horse breeds and has led to the replacement of autochthonous Y chromosomes. Only a few northern European breeds bear unique variants at high frequencies or fixed within but not shared among breeds. Our Y-chromosomal data complement the well established mtDNA lineages and document the male side of the genetic history of modern horse breeds and breeding practices.     

Population Differentiation of Southern Indian Male Lineages Correlates with Agricultural Expansions Predating the Caste System

Previous studies that pooled Indian populations from a wide variety of geographical locations, have obtained contradictory conclusions about the processes of the establishment of the Varna caste system and its genetic impact on the origins and demographic histories of Indian populations. To further investigate these questions we took advantage that both Y chromosome and caste designation are paternally inherited, and genotyped 1,680 Y chromosomes representing 12 tribal and 19 non-tribal (caste) endogamous populations from the predominantly Dravidian-speaking Tamil Nadu state in the southernmost part of India. Tribes and castes were both characterized by an overwhelming proportion of putatively Indian autochthonous Y-chromosomal haplogroups (H-M69, F-M89, R1a1-M17, L1-M27, R2-M124, and C5-M356; 81% combined) with a shared genetic heritage dating back to the late Pleistocene (10–30 Kya), suggesting that more recent Holocene migrations from western Eurasia contributed <20% of the male lineages. We found strong evidence for genetic structure, associated primarily with the current mode of subsistence. Coalescence analysis suggested that the social stratification was established 4–6 Kya and there was little admixture during the last 3 Kya, implying a minimal genetic impact of the Varna (caste) system from the historically-documented Brahmin migrations into the area. In contrast, the overall Y-chromosomal patterns, the time depth of population diversifications and the period of differentiation were best explained by the emergence of agricultural technology in South Asia. These results highlight the utility of detailed local genetic studies within India, without prior assumptions about the importance of Varna rank status for population grouping, to obtain new insights into the relative influences of past demographic events for the population structure of the whole of modern India.     

On the Male Genital Armature in the European Rhopalocera.

IN several orders of the Insecta the structure of the organs upon which the perpetuation of the species depends has afforded, in very many cases, the best and surest characters for the discrimination of species. But in the Lepidoptera, one of the largest of the orders, and that on which perhaps the greatest amount of attention (scientific or otherwise) has been bestowed, the structure of these parts has not received the consideration it deserves, but has been almost entirely ignored. The author in confining himself to the European forms is not prepared to admit that his conclusions thereon will hold good with the Lepidoptera in general, though there are certain indications that it may. He has selected Epinephele hyperantus, L., as a type or standard, and describes its apical segment, noting that in this and all cases it is necessary to clear away the scales and hairs for a clear and satisfactory view of the parts to be obtained. The appendages are three, viz. a superior and two lateral ones. To the latter he applies the name “ harpagones,” though possibly equivalents of the appendices inferiores in Trichoptera. The upper appendage he designates “ tegumen;” and he takes notice of the relations of all three to the anal opening and intromittent organ &c.‘ He has discussed the structure of the apical segment, and its modifications in various families, the nature and varied character of the tegumen and of the harpagones, comparing the resemblances and differences in groups. Prom these data he then traces the apparent affinities as derived from the said characters, and gives it as his opinion that not only do they yield good generic distinctions, but that in many cases specific differentiation is very appreciable. In his researches the author has made a great number of sketches, which illustrations render comparison relatively easy. These and the complete paper will hereafter be published in the Society's ‘Transactions’     

Circulation of Different Lineages of Dengue Virus 2, Genotype American/Asian in Brazil: Dynamics and Molecular and Phylogenetic Characterization

The American/Asian genotype of Dengue virus type 2 (DENV-2) was introduced into the Americas in the 80′s. Although there is no data showing when this genotype was first introduced into Brazil, it was first detected in Brazil in 1990. After which the virus spread throughout the country and major epidemics occurred in 1998, 2007/08 and 2010. In this study we sequenced 12 DENV-2 genomes obtained from serum samples of patients with dengue fever residing in São José do Rio Preto, São Paulo (SJRP/SP), Brazil, in 2008. The whole open reading frame or envelope sequences were used to perform phylogenetic, phylogeographic and evolutionary analyses. Isolates from SJRP/SP were grouped within one lineage (BR3) close to isolates from Rio de Janeiro, Brazil. Isolates from SJRP were probably introduced there at least in 2007, prior to its detection in the 2008 outbreak. DENV-2 circulation in Brazil is characterized by the introduction, displacement and circulation of three well-defined lineages in different times, most probably from the Caribbean. Thirty-seven unique amino acid substitutions were observed among the lineages, including seven amino acid differences in domains I to III of the envelope protein. Moreover, we dated here, for the first time, the introduction of American/Asian genotype into Brazil (lineage BR1) to 1988/89, followed by the introduction of lineages BR2 (1998–2000) and BR3 (2003–05). Our results show a delay between the introduction and detection of DENV-2 lineages in Brazil, reinforcing the importance and need for surveillance programs to detect and trace the evolution of these viruses. Additionally, Brazilian DENV-2 differed in genetic diversity, date of introduction and geographic origin and distribution in Brazil, and these are important factors for the evolution, dynamics and control of dengue.     

Absence of Positive Selection on Centromeric Histones in Tetrahymena Suggests Unsuppressed Centromere-Drive in Lineages Lacking Male Meiosis

Centromere-drive is a process where centromeres compete for transmission through asymmetric "female" meiosis for inclusion into the oocyte. In symmetric "male" meiosis, all meiotic products form viable germ cells. Therefore, the primary incentive for centromere-drive, a potential transmission bias, is believed to be missing from male meiosis. In this article, we consider whether male meiosis also bears the primary cost of centromere-drive. Because different taxa carry out different combinations of meiotic programs (symmetric?+?asymmetric, symmetric only, asymmetric only), it is possible to consider the evolutionary consequences of centromere-drive in the context of these differing systems. Groups with both types of meiosis have large, rapidly evolving centromeric regions, and their centromeric histones (CenH3s) have been shown to evolve under positive selection, suggesting roles as suppressors of centromere-drive. In contrast, taxa with only symmetric male meiosis have shown no evidence of positive selection in their centromeric histones. In this article, we present the first evolutionary analysis of centromeric histones in ciliated protozoans, a group that only undergoes asymmetric "female" meiosis. We find no evidence of positive selection acting on CNA1, the CenH3 of Tetrahymena species. Cytological observations of a panel of Tetrahymena species are consistent with dynamic karyotype evolution in this lineage. Our findings suggest that defects in male meiosis, and not mitosis or female meiosis, are the primary selective force behind centromere-drive suppression. Our study raises the possibility that taxa like ciliates, with only female meiosis, may therefore undergo unsuppressed centromere drive.     

Admixture and Gene Flow from Russia in the Recovering Northern European Brown Bear (Ursus arctos)

Large carnivores were persecuted to near extinction during the last centuries, but have now recovered in some countries. It has been proposed earlier that the recovery of the Northern European brown bear is supported by migration from Russia. We tested this hypothesis by obtaining for the first time continuous sampling of the whole Finnish bear population, which is located centrally between the Russian and Scandinavian bear populations. The Finnish population is assumed to experience high gene flow from Russian Karelia. If so, no or a low degree of genetic differentiation between Finnish and Russian bears could be expected. We have genotyped bears extensively from all over Finland using 12 validated microsatellite markers and compared their genetic composition to bears from Russian Karelia, Sweden, and Norway. Our fine masked investigation identified two overlapping genetic clusters structured by isolation-by-distance in Finland (pairwise F_ST = 0.025). One cluster included Russian bears, and migration analyses showed a high number of migrants from Russia into Finland, providing evidence of eastern gene flow as an important driver during recovery. In comparison, both clusters excluded bears from Sweden and Norway, and we found no migrants from Finland in either country, indicating that eastern gene flow was probably not important for the population recovery in Scandinavia. Our analyses on different spatial scales suggest a continuous bear population in Finland and Russian Karelia, separated from Scandinavia.     

Intercontinental Mediterranean disjunct mosses: morphological and molecular patterns

This study focused on three species that occur disjunctly between western North America and the Mediterranean region of southern Europe, northern Africa, and western Asia, forming the so-called Madrean-Tethyan distribution pattern. Quantitative morphological characters were measured in New and Old World plants to find any subtle phenotypic differentiation between the disjunct populations. Sequences from the nuclear ribosomal internal transcribed spacer region were obtained from the same populations to assess differentiation at the molecular level and to compare molecular diversity with patterns of morphological similarity among plants. Little or no morphological differentiation existed between New and Old World plants in any of the species, but internal transcribed spacer (ITS) sequences revealed some phylogeographic structure. Patterns of morphological similarity in all three species were incongruent with phylogeographic structure revealed by sequence data. New World populations were more variable than Old World populations at the molecular level in the three species. Despite some evidence for differentiation between disjunct plants, no plausible mutation rate would date the divergence at ≥20 million years ago (MYA), as implied by the Madrean-Tethyan hypothesis. Recent long-distance dispersal is a more likely explanation for intercontinental disjunctions in these species.     

Genomic Admixture Analysis in European Populus spp. Reveals Unexpected Patterns of Reproductive Isolation and Mating

Admixture between genetically divergent populations facilitates genomic studies of the mechanisms involved in adaptation, reproductive isolation, and speciation, including mapping of the loci involved in these phenomena. Little is known about how pre- and postzygotic barriers will affect the prospects of “admixture mapping” in wild species. We have studied 93 mapped genetic markers (microsatellites, indels, and sequence polymorphisms, ∼60,000 data points) to address this topic in hybrid zones of Populus alba and P. tremula, two widespread, ecologically important forest trees. Using genotype and linkage information and recently developed analytical tools we show that (1) reproductive isolation between these species is much stronger than previously assumed but this cannot prevent the introgression of neutral or advantageous alleles, (2) unexpected genotypic gaps exist between recombinant hybrids and their parental taxa, (3) these conspicuous genotypic patterns are due to assortative mating and strong postzygotic barriers, rather than recent population history. We discuss possible evolutionary trajectories of hybrid lineages between these species and outline strategies for admixture mapping in hybrid zones between highly divergent populations. Datasets such as this one are still rare in studies of natural hybrid zones but should soon become more common as high throughput genotyping and resequencing become feasible in nonmodel species.ADMIXTURE or hybrid zones between genetically divergent populations are increasingly being explored for their use in studies of adaptation, reproductive isolation, and speciation (Rieseberg et al. 1999; Martinsen et al. 2001; Wu 2001; Vines et al. 2003; Payseur et al. 2004; reviewed by Coyne and Orr 2004), especially for their potential in identifying recombinants for gene mapping (otherwise known as “admixture mapping”; Chakraborty and Weiss 1988; Briscoe et al. 1994; Rieseberg et al. 1999; Reich et al. 2005; Slate 2005; Zhu et al. 2005; Lexer et al. 2007; Nolte et al. 2009). In many taxa of animals and plants, recombinants are created by admixture between divergent populations or species in hybrid zones or ecotones (Buerkle and Lexer 2008; Gompert and Buerkle 2009). The growing interest of evolutionary geneticists in admixture has its roots in both basic evolutionary genetics and breeding.With respect to evolutionary genetics, admixed populations have been viewed as important resources for studying the genetics of adaptation and speciation, since the discovery that by fitting geographical clines of allele frequencies across hybrid zones, the strength of intrinsic and extrinsic (ecological) barriers to gene flow can be estimated (Barton and Hewitt 1985; Barton and Gale 1993). More recently, the genomics era has taken these concepts to a new level by providing genetic or physical genome maps for many species so that clines or introgression patterns of individual loci can be compared to their genomic background (see below; Falush et al. 2003; Gompert and Buerkle 2009). Thus, hybrid zones permit the identification and study of quantitative trait loci (QTL), genes, or other genetic elements involved in reproductive isolation and speciation in situ, directly in natural populations, if sufficient genetic recombination has occurred (Rieseberg and Buerkle 2002). In applied genetics, studies of hybrid zones yield information on the genomic architecture of barriers to introgression, which is of great interest to breeders concerned with the establishment of pedigrees for tree selection and domestication (Stettler et al. 1996).Most animal or plant hybrid zones studied to date involve hybridization between parental populations that are much more divergent than the admixed human populations that have been used successfully for gene mapping in human medical genetics (e.g., Reich et al. 2005; Zhu et al. 2005). Little experience exists with interpreting genomic patterns of ancestry and admixture in such highly divergent, nonhuman populations. Early genomic work on hybrid zones, based on dominant genetic markers, suggested the feasibility of mapping genome regions involved in reproductive isolation and speciation (Rieseberg et al. 1999; Rogers et al. 2001), but these studies did not allow tests for selection on genotypes at single loci in different genomic backgrounds. This became possible only recently due to the development of novel analytical tools suited to large numbers of codominant markers, especially linkage models of Bayesian admixture analysis (Falush et al. 2003, 2007) and methods to fit “genomic clines” of codominant marker genotypes across complete genomic admixture gradients (Lexer et al. 2007; Gompert and Buerkle 2009; Nolte et al. 2009; Teeter et al. 2010). Great advances also have been made in interpreting single-locus estimates of genetic divergence between populations and species (Beaumont 2005; Foll and Gaggiotti 2008; Excoffier et al. 2009a). Here, we bring these approaches together to yield novel insights into genomic patterns of reproductive isolation and mating in hybrid zones of two widespread and important members of the “model tree” genus Populus. Our goal was to infer patterns of reproductive isolation and the likely evolutionary trajectories of hybrid populations and to develop strategies for genetic mapping in admixed populations.Populus alba (white poplar) and P. tremula (European aspen) are ecologically divergent (floodplain vs. upland habitat) hybridizing tree species related to P. trichocarpa, the first completely sequenced forest tree (Tuskan et al. 2006). The two species are highly differentiated for neutral DNA-based markers (Lexer et al. 2007) and numerous phenotypic and ecological traits (Lexer et al. 2009). Mosaic hybrid zones between these species often form in riparian habitats (Lexer et al. 2005; hybrids sometimes referred to as P. × canescens) and have been proposed as potential “mapping populations” for identifying QTL and genes of interest in evolutionary biology (Lexer et al. 2007; Buerkle and Lexer 2008) and breeding (Fossati et al. 2004; Lexer et al. 2004). Previous studies of these hybrid zones were conducted with a relatively small number of genetic markers and without making use of linkage information; the genomic composition of hybrid zones between these species has never been studied with a genomewide panel of codominant markers with known linkage relationships. Specifically, we address the following questions in this contribution:(1) What does an analysis of admixture and differentiation based on a genome-wide panel of mapped markers tell us about patterns of reproductive isolation and mating in hybrid zones of European Populus species? (2) What are the likely roles of pre- and postzygotic barriers vs. recent, localized historical factors in generating the observed genomic patterns? (3) What are the practical implications for admixture mapping in hybrid zones between highly divergent populations? We showcase where the genetic peculiarities of hybrid zones will limit their use for gene mapping and where they suggest new approaches that were perhaps not foreseen by geneticists with a focus on human medical applications.     

MtDNA and Y-Chromosome Lineages in the Yakut Population

The structure of female (mtDNA) and male (Y-chromosome haplotypes) lineages in the Yakut population was examined. To determine mtDNA haplotypes, sequencing of hypervariable segment I and typing of haplotype-specific point substitutions in the other parts of the mtDNA molecule were performed. Y haplogroups were identified through typing of biallelic polymorphisms in the nonrecombining part of the chromosome. Haplotypes within haplogroups were analyzed with seven microsatellite loci. Mitochondrial gene pool of Yakuts is mainly represented by the lineages of eastern Eurasian origin (haplogroups A, B, C, D, G, and F). In Yakuts haplogroups C and D showing the total frequency of almost 80% and consisting of 12 and 10 different haplopypes, respectively, were the most frequent and diverse. The total part of the lineages of western Eurasian origin (Caucasoid) was about 6% (4 haplotypes, haplogroups H, J, and U). Most of Y chromosomes in the Yakut population (87%) belonged to haplogroup N3 (HG16), delineated by the T–C substitution at the Tat locus. Chromosomes of haplogroup N3 displayed the presence of 19 microsatellite haplotypes, the most frequent of which encompassed 54% chromosomes of this haplogroup. Median network of haplogroup N3 in Yakuts demonstrated distinct starlike phylogeny. Male lineages of Yakuts were shown to be closest to those of Eastern Evenks.     

Neofunctionalization of Duplicated Tic40 Genes Caused a Gain-of-Function Variation Related to Male Fertility in Brassica oleracea Lineages

Gene duplication followed by functional divergence in the event of polyploidization is a major contributor to evolutionary novelties. The Brassica genus evolved from a common ancestor after whole-genome triplication. Here, we studied the evolutionary and functional features of Brassica spp. homologs to Tic40 (for translocon at the inner membrane of chloroplasts with 40 kDa). Four Tic40 loci were identified in allotetraploid Brassica napus and two loci in each of three basic diploid Brassica spp. Although these Tic40 homologs share high sequence identities and similar expression patterns, they exhibit altered functional features. Complementation assays conducted on Arabidopsis thaliana tic40 and the B. napus male-sterile line 7365A suggested that all Brassica spp. Tic40 homologs retain an ancestral function similar to that of AtTic40, whereas BolC9.Tic40 in Brassica oleracea and its ortholog in B. napus, BnaC9.Tic40, in addition, evolved a novel function that can rescue the fertility of 7365A. A homologous chromosomal rearrangement placed bnac9.tic40 originating from the A genome (BraA10.Tic40) as an allele of BnaC9.Tic40 in the C genome, resulting in phenotypic variation for male sterility in the B. napus near-isogenic two-type line 7365AB. Assessment of the complementation activity of chimeric B. napus Tic40 domain-swapping constructs in 7365A suggested that amino acid replacements in the carboxyl terminus of BnaC9.Tic40 cause this functional divergence. The distribution of these amino acid replacements in 59 diverse Brassica spp. accessions demonstrated that the neofunctionalization of Tic40 is restricted to B. oleracea and its derivatives and thus occurred after the divergence of the Brassica spp. A, B, and C genomes.Polyploidy or whole-genome duplication is thought to be a prominent evolutionary force in eukaryotes (Wolfe, 2001; Udall and Wendel, 2006), especially for flowering plants (Blanc and Wolfe, 2004; Van de Peer et al., 2009). Almost 95% of angiosperms show evidence of having undergone at least one round of whole-genome duplication in their evolutionary history, suggesting that most extant diploid flowering plants have evolved from ancient polyploids (Cui et al., 2006; Soltis et al., 2009). Gene duplications in the event of polyploidization provide sources for evolutionary novelties that could benefit plants (Lukens et al., 2004; Chen, 2007). Divergence after gene duplication could result in three primary evolutionary fates of duplicated genes: pseudogenization, neofunctionalization, and subfunctionalization (Force et al., 1999; Conant and Wolfe, 2008; Liu and Adams, 2010). Pseudogenization implies that duplicated genes with redundant functions lose their function by accumulating negative mutations; neofunctionalization denotes that the redundant gene evolves a new adaptive function; while subfunctionalization causes the duplicated genes to adopt a different part of the function of an ancestral gene (Rodríguez-Trelles et al., 2003; Flagel and Wendel, 2009; Liu and Adams, 2010).The Brassica genus consists of three basic diploid species: Brassica rapa (AA; n = 10), Brassica nigra (BB; n = 8), and Brassica oleracea (CC; n = 9), and their derivative allotetraploid species: Brassica juncea (AABB; n = 18), Brassica napus (AACC; n = 19), and Brassica carinata (BBCC; n = 17; Beilstein et al., 2006). Comparative genetic mapping demonstrated that these Brassica spp., which diverged from Arabidopsis thaliana approximately 20 to 40 million years ago (Lagercrantz and Lydiate, 1996; Blanc et al., 2003; Town et al., 2006), descended from a common ancestor after whole-genome triplication (Parkin et al., 2002). Collinear comparison showed that for each of 24 ancestral genomic blocks defined in the ancestral karyotype in A. thaliana, three syntenic copies were identified in each of the diploid Brassica spp. genomes, with only one exception (Schranz et al., 2006; Wang et al., 2011; Cheng et al., 2013). Fractionation (gene loss from homologous genomic regions) and chromosomal rearrangements were prevalent in the diploidization process of the hexaploid Brassica spp. common ancestor (Lagercrantz, 1998; Town et al., 2006; Ziolkowski et al., 2006; Mun et al., 2009). Based on gene density differences caused by varying gene loss rates in the three collinear genomic block copies, these genomic blocks were classified into three subgenomes in the diploid Brassica spp. genomes: the least fractionated (LF), the medium fractionated (MF1), and the most fractionated (MF2) subgenomes (Wang et al., 2011; Tang and Lyons, 2012; Cheng et al., 2013). The different rates of gene loss of the three subgenomes support a two-step origin of the Brassiceae ancestral genome involving a tetraploidization process followed by substantial fractionation of the subgenomes MF1 and MF2 and more recently hybridization with the third subgenome LF to form a hexaploid (Wang et al., 2011; Tang et al., 2012). Although collinearity and changes in genomic structure, including duplications, deletions, and rearrangements of the Brassica spp. and A. thaliana are well studied, there is limited knowledge of the molecular and functional divergence of duplicated or homologous genes in the Brassica spp.To utilize heterosis in B. napus breeding, hybrid production is based mainly on male sterility. Currently, the recessive epistatic genic male-sterile three-type line system 7365ABC is widely used for oilseed heterosis due to its advantages, producing 100% sterile offspring for realizing the triple-cross hybrid (Huang et al., 2007; Xia et al., 2012). The male sterility in this system is controlled by two genes, a recessive male sterile gene Bnms3 and a epistatic gene BnRf (Zhou et al., 2012). Bnms3 was recently reported to be a homolog to A. thaliana Tic40 (Dun et al., 2011). Tic40 was identified as a member of the TIC (for translocon at the inner envelope membrane of chloroplasts) complex that functions as a cochaperone to coordinate Tic110 and the stromal chaperone heat shock protein93 (Hsp93) (Chou et al., 2003, 2006). The A. thaliana tic40 mutant displayed a chlorotic phenotype throughout development (Chou et al., 2003) but a male-fertile phenotype with mature pollen grains (Dun et al., 2011). Interestingly, one allele of Bnms3, BnaC.Tic40, can rescue the fertility of the B. napus male-sterile line 7365A (Dun et al., 2011).In this study, we identified and characterized Tic40 homologs in B. napus and three basic diploid Brassica spp. We suggested that neofunctionalization of BnaC9.Tic40 after the divergence of the Brassica spp. A, B, and C genomes was caused by amino acid replacements in the C terminus of BnaC9.Tic40. In addition, we validated that the allelic genes BnaC9.Tic40 (equivalent to BnaC.Tic40 as described by Dun et al. [2011]) and bnac9.tic40 originate from the C and A genomes, respectively, and became allelic due to a homologous chromosomal rearrangement in B. napus. These results provide further knowledge for the effective utilization of the restoring gene of 7365A and a better insight into the functional divergence of homologous duplicated genes in paleoploid Brassica spp.     

RBR Ubiquitin Ligases: Diversification and Streamlining in Animal Lineages

The patterns of emergence and disappearance in animal species of genes encoding RBR ubiquitin ligases are described. RBR genes can be classified into subfamilies (Parkin, Ariadne, Dorfin, ARA54, etc.) according to sequence and structural data. Here, I show that most animal-specific RBR subfamilies emerged early in animal evolution, and that ancient animals, before the cnidarian/bilaterian split, had a set of RBR genes, which was as complex as the one currently found in mammals. However, some lineages (nematodes, dipteran insects) have recently suffered multiple losses, leading to a highly simplified set of RBR genes. Genes of a particular RBR subfamily, characterized by containing a helicase domain and so far found only in plants, are present also in some animal species. The meaning of these patterns of diversification and streamlining are discussed at the light of functional data. Extreme evolutionary conservation may be related to gene products having housekeeping functions. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Defining Cell Lineages in the Prostate Epithelium

Understanding the stages of cell differentiation in the normal prostate epithelium isessential for the identification of the cell type(s) involved in prostatic carcinogenesis.Prostate glands are composed of three types of epithelial cells (i.e. basal, secretory andneuroendocrine) but the hierarchical relations among these cell types have been longcontroversial. We have recently developed a novel system to define prostate epithelialcell lineages in vivo. We find that, during normal prostate organogenesis, terminallydifferentiated secretory cells derive from p63-positive basal cells, which thusrepresent/include prostate stem cells. Future studies will determine if p63-positive basalcells retain stem cells capabilities in the adult prostate epithelium.     

Cryptic Lineages of the Genus Escherichia

Extended multilocus sequence typing (MLST) analysis of atypical Escherichia isolates was used to identify five novel phylogenetic clades (CI to CV) among isolates from environmental, human, and animal sources. Analysis of individual housekeeping loci showed that E. coli and its sister clade, CI, remain largely indistinguishable and represent nascent evolutionary lineages. Conversely, clades of similar age (CIII and CIV) were found to be phylogenetically distinct. When all Escherichia lineages (named and unnamed) were evaluated, we found evidence that Escherichia fergusonii has evolved at an accelerated rate compared to E. coli, CI, CIII, CIV, and CV, suggesting that this species is younger than estimated by the molecular clock method. Although the five novel clades were phylogenetically distinct, we were unable to identify a discriminating biochemical marker for all but one of them (CIII) with traditional phenotypic profiling. CIII had a statistically different phenotype from E. coli that resulted from the loss of sucrose and sorbitol fermentation and lysine utilization. The lack of phenotypic distinction has likely hindered the ability to differentiate these clades from typical E. coli, and so their ecological significance and importance for applied and clinical microbiology are yet to be determined. However, our sampling suggests that CIII, CIV, and CV represent environmentally adapted Escherichia lineages that may be more abundant outside the host gastrointestinal tract.It almost goes without saying that Escherichia coli is an important model organism and has been for more than 120 years. E. coli is often used to study bacterial adaptation (49), experimental evolution (9, 36), and speciation (11, 28, 33, 43). Comparisons between representative genomes continue to provide valuable information about these processes (58), and as genetic data accumulate, our understanding of how bacteria adapt to change and evolve is clarified. For example, E. coli lineages do not easily fit a biological species concept (43), as was previously suggested (11), so it may be more practical to identify lineages that share similar ecological niches rather than phylogenetic similarity alone (27).E. coli adaptation to the gastrointestinal (GI) tract of warm-blooded animals is largely considered to be the most important source of natural selection during its evolution from a common ancestor with Salmonella. E. coli was originally discovered in and has long been associated with the indigenous microbiota of the GI tract of humans and animals. The vast majority of E. coli organisms transiently pass through the GI tract with little or no effect on the host (6, 46). A small number are able to establish and persist within a single host for months and years, presumably because of symbiotic relationships that develop with other constituents of the microbiota. Some isolates that reach the GI tract are pathogenic and are responsible for a variety of symptoms involving both intestinal and extraintestinal infections of humans and animals. Every year there are approximately 1 billion episodes of diarrhea among children under the age of 5 in developing countries, and 2 million of these cases result in death (35). Pathogenic E. coli is the most common bacterial cause of acute diarrhea in this pediatric population (35), making it a leading cause of diarrhea-associated deaths worldwide. The primary route of transmission for some E. coli, especially pathogenic lineages like Shigella spp., is thought to be the fecal-oral route. This observation underlies its global use as an indicator of water quality as well as its use in microbial source tracking studies whose aim is to determine the source of fecal contamination.What is known about E. coli ecology (i.e., its abundance and distribution and the factors that influence them) is based on data from studies of representative isolates. For two main reasons, historical collections of isolates hold the potential for misleading conclusions. First, when isolates are assembled for analyses, most studies begin by confirming a phenetic species definition (50) (i.e., lactose fermentation, indole production, or lack of citrate utilization). All isolates that fit this definition are included even though they may not fit an alternative species definition, such as one based on phylogenetics (52). Second, the way that samples have been collected has not been uniform across habitats where E. coli is commonly found. A disproportionately large amount of data has been collected from E. coli isolated from humans and domesticated animals. Therefore, there is potential for under-sampled phenotypic and genotypic diversity from non-host-associated habitats, like the environment (5, 15, 59).Characterizations of isolates from the environment are changing the way we view E. coli life history. A number of studies have found stable genotypes in the environment, suggesting that certain populations readily circulate and persist outside the host GI tract (5, 15, 24, 40, 59, 61, 62). These observations support the hypothesis that a significant proportion of the global E. coli population is not transmitted directly between hosts via the fecal-oral route but instead flow between the environment and hosts. In this study, we present the identification and genetic characterization of five novel Escherichia clades. Using extended multilocus sequence typing (MLST) analysis, we show that representative isolates formed highly supported and distinct genetic clusters. On the basis of biochemical profiling, we found that the clades were highly similar in phenotype and could not be easily distinguished from E. coli. We used PCR screening of genes in the E. coli pan-genome to show that there has been recent gene flow between E. coli and all other Escherichia species and clades and that the percentages of shared loci among clades were not well correlated with the sequence divergence between them. We also show that Escherichia species and clades differ in their rates of evolution and that the species Escherichia fergusonii appears to be evolving under nonneutral conditions. Lastly, since some of the clades appear to be overrepresented in habitats outside of the host GI tract, we discuss their potential importance and how they may add to our biological understanding of the model organism, E. coli.     

Individual Male Calling Pattern and Male Mating Success in the European Treefrog (Hyla arborea): Is there Evidence for Directional or Stabilizing Selection on Male Calling Behaviour?

In anurans, call properties are commonly classified based on within‐male variability as being either static or dynamic. Numerous playback experiments in the laboratory have indicated that female preferences based on dynamic call properties are usually strongly directional, while female preferences based on static call properties are often stabilizing or weakly directional. However, there are only few studies demonstrating that female preferences for high values of dynamic call properties indeed exert directional selection on male calling behaviour in natural populations. Moreover, field studies investigating whether female preferences for values of static call properties around the mean of the population lead to currently operating stabilizing selection on male calling patterns in natural populations are completely lacking. Here I investigate for two consecutive breeding seasons male calling patterns and male mating success in a population of individually marked European treefrogs (Hyla arborea), a hylid frog with prolonged breeding season and a lek mating system. Individual male calling pattern as analysed in terms of seven temporal and spectral call properties did not differ between males that survived from one breeding season to the next and those not surviving. None of the seven call properties investigated differed significantly between mated and unmated males, indicating that there is no strong directional selection on male calling behaviour in the study population. However, in one study season males that produced calls with a number of pulses around the mean of the population were significantly more likely to obtain matings than males that produced calls with a number of pulses at the low or high end of the distribution. Thus, this study provides preliminary evidence for the operation of stabilizing selection on a static call property (i.e. the number of pulses per call) in a natural population of an anuran amphibian.