Genetic patterns and changes in availability of suitable habitat support a colonisation history of a North American perennial plant.

Climatic fluctuations during the Pleistocene influenced the geographical distribution of plant species across the southern region of California. Following an integrative approach, we combined genetic data analysis with Environmental Niche Models (ENMs) to assess the historical range expansion of Yucca schidigera, a long-lived desert perennial native of the Baja California Peninsula. We genotyped 240 individuals with seven nuclear microsatellite to investigate genetic diversity distribution across 13 populations. Indeed, we used Environmental Niche Models to examine the changes on the distribution of suitable climatic conditions for this species during the LIG (~120 ka), LGM (~22 ka) and Mid Holocene (~6 ka). We detected high genetic diversity across Y. schidigera populations (AR = 9.94 ± 0.38 SE; Hexp = 0.791 ± 0.011 SE) with genetic variation decreasing significantly with latitude (allelic richness: R 2 = 0.38, P = 0.023; expected heterocigosity: R2 = 0.32, P = 0.042). We observed low, but significant genetic differentiation (FST = 0.0678; P < 0.001) which was consistent with the parapatric distribution of the three genetic groupings detected by the Bayesian clustering algorithm. The ENMs suggest that suitable habitat for this species increased since the LGM. Our results support a range expansion of Y. schidigera across northwestern Baja California during the late Quaternary. Genetic data suggest that colonization of the current distribution followed a southward directionality as suitable climatic conditions became widely available in this region. High genetic variation across our sample suggests large historic effective population sizes for this section of the geographical range.

Tempo and mode in coevolution of Agave sensu lato (Agavoideae, Asparagaceae) and its bat pollinators, Glossophaginae (Phyllostomidae).

The genus Agave sensu lato contains ca. 211 described species, many of which are considered keystone species because of their ecological dominance and the quantity of resources they provide with their massive, nectar-rich inflorescences. The large diversity of Agave species has been hypothesized as being related to their reproductive strategy (predominantly monocarpic) and diverse pollinators (e.g., bats, hummingbirds, hawkmoths). In particular, Agave species provide resources that a few genera of nectar feeding bats from the subfamily Glosophaginae are dependent upon. To explore a possible coevolutionary relationship between Agave and the bat species that pollinate them, we calibrated molecular phylogenies of both groups and looked for a correlation in their dates of divergence. One coding and two non-coding regions of the chloroplast genome were sequenced from 49 species of the Agavoideae (Asparagaceae), and the mitochondrial gene Cyt-b and nuclear coding gene RAG2 were either sequenced or obtained from gene bank for 120 Phyllostomid bats. Results from the analyses indicate that Agave sensu lato is a young genus (estimated crown age 2.7-8.5/stem age 4.6-12.3 Ma), with an increasing diversification rate, and the highest speciation rate among Agavoideae's clades. The origin of the Glossophaginae bats (stem age 20.3-23.5 Ma) occurred prior to the stem age of Agave sensu lato, while the origin of the current pollinators of Agave species, members of the genera Glossophaga, Leptonycteris, Anoura, Choeronyscus, Musonycteris and Choeronycteris, was estimated to be around 6.3-16.2 Ma, overlapping with the stem age of Agave sensu lato, supporting the hypothesis of diffuse coevolution.

The Geographic Structure of Viruses in the Cuatro Ciénegas Basin, a Unique Oasis in Northern Mexico, Reveals a Highly Diverse Population on a Small Geographic Scale.

The Cuatro Ciénegas Basin (CCB) is located in the Chihuahuan desert in the Mexican state of Coahuila; it has been characterized as a site with high biological diversity despite its extreme oligotrophic conditions. It has the greatest number of endemic species in North America, containing abundant living microbialites (including stromatolites and microbial mats) and diverse microbial communities. With the hypothesis that this high biodiversity and the geographic structure should be reflected in the virome, the viral communities in 11 different locations of three drainage systems, Churince, La Becerra, and Pozas Rojas, and in the intestinal contents of 3 different fish species, were analyzed for both eukaryotic and prokaryotic RNA and DNA viruses using next-generation sequencing methods. Double-stranded DNA (dsDNA) virus families were the most abundant (72.5% of reads), followed by single-stranded DNA (ssDNA) viruses (2.9%) and ssRNA and dsRNA virus families (0.5%). Thirteen families had dsDNA genomes, five had ssDNA, three had dsRNA, and 16 had ssRNA. A highly diverse viral community was found, with an ample range of hosts and a strong geographical structure, with very even distributions and signals of endemicity in the phylogenetic trees from several different virus families. The majority of viruses found were bacteriophages but eukaryotic viruses were also frequent, and the large diversity of viruses related to algae were a surprise, since algae are not evident in the previously analyzed aquatic systems of this ecosystem. Animal viruses were also frequently found, showing the large diversity of aquatic animals in this oasis, where plants, protozoa, and archaea are rare.IMPORTANCE In this study, we tested whether the high biodiversity and geographic structure of CCB is reflected in its virome. CCB is an extraordinarily biodiverse oasis in the Chihuahuan desert, where a previous virome study suggested that viruses had followed the marine ancestry of the marine bacteria and, as a result of their long isolation, became endemic to the site. In this study, which includes a larger sequencing coverage and water samples from other sites within the valley, we confirmed the high virus biodiversity and uniqueness as well as the strong biogeographical diversification of the CCB. In addition, we also analyzed fish intestinal contents, finding that each fish species eats different prey and, as a result, presents different viral compositions even if they coexist in the same pond. These facts highlight the high and novel virus diversity of CCB and its "lost world" status.

Connecting genomic patterns of local adaptation and niche suitability in teosintes.

The central abundance hypothesis predicts that local adaptation is a function of the distance to the centre of a species' geographic range. To test this hypothesis, we gathered genomic diversity data from 49 populations, 646 individuals and 33,464 SNPs of two wild relatives of maize, the teosintes Zea mays ssp. parviglumis and Zea. mays. ssp. mexicana. We examined the association between the distance to their climatic and geographic centroids and the enrichment of SNPs bearing signals of adaptation. We identified candidate adaptive SNPs in each population by combining neutrality tests and cline analyses. By applying linear regression models, we found that the number of candidate SNPs is positively associated with niche suitability, while genetic diversity is reduced at the limits of the geographic distribution. Our results suggest that overall, populations located at the limit of the species' niches are adapting locally. We argue that local adaptation to this limit could initiate ecological speciation processes and facilitate adaptation to global change.

Signatures of local adaptation in lowland and highland teosintes from whole-genome sequencing of pooled samples.

Spatially varying selection triggers differential adaptation of local populations. Here, we mined the determinants of local adaptation at the genomewide scale in the two closest maize wild relatives, the teosintes Zea mays ssp parviglumis and ssp. mexicana. We sequenced 120 individuals from six populations: two lowland, two intermediate and two highland populations sampled along two altitudinal gradients. We detected 8 479 581 single nucleotide polymorphisms (SNPs) covered in the six populations with an average sequencing depth per site per population ranging from 17.0× to 32.2×. Population diversity varied from 0.10 to 0.15, and linkage disequilibrium decayed very rapidly. We combined two differentiation-based methods, and correlation of allele frequencies with environmental variables to detect outlier SNPs. Outlier SNPs displayed significant clustering. From clusters, we identified 47 candidate regions. We further modified a haplotype-based method to incorporate genotype uncertainties in haplotype calling, and applied it to candidate regions. We retrieved evidence for selection at the haplotype level in 53% of our candidate regions, and in 70% of the cases the same haplotype was selected in the two lowland or the two highland populations. We recovered a candidate region located within a previously characterized inversion on chromosome 1. We found evidence of a soft sweep at a locus involved in leaf macrohair variation. Finally, our results revealed frequent colocalization between our candidate regions and loci involved in the variation of traits associated with plant-soil interactions such as root morphology, aluminium and low phosphorus tolerance. Soil therefore appears to be a major driver of local adaptation in teosintes.

Nitrogen fixation in microbial mat and stromatolite communities from Cuatro Cienegas, Mexico.

Nitrogen fixation (nitrogenase activity, NA) of a microbial mat and a living stromatolite from Cuatro Cienegas, Mexico, was examined over spring, summer, and winter of 2004. The goal of the study was to characterize the diazotrophic community through molecular analysis of the nifH gene and using inhibitors of sulfate reduction and oxygenic and anoxygenic photosynthesis. We also evaluated the role of ultraviolet radiation on the diazotrophic activity of the microbial communities. Both microbial communities showed patterns of NA with maximum rates during the day that decreased significantly with 3-3,4-dichlorophenyl-1',1'-dimethylurea, suggesting the potential importance of heterocystous cyanobacteria. There is also evidence of NA by sulfur-reducing bacteria in both microbial communities suggested by the negative effect exerted by the addition of sodium molybdate. Elimination of infrared and ultraviolet radiation had no effect on NA. Both microbial communities had nifH sequences that related to group I, including cyanobacteria and purple sulfur and nonsulfur bacteria, as well as group II nitrogenases, including sulfur reducing and green sulfur bacteria.

Genetic differentiation in the Agave deserti (Agavaceae) complex of the Sonoran desert.

The Agave deserti complex, comprising A. deserti, A. cerulata and A. subsimplex, represents a group of species and subspecies with a near allopatric distribution and clear differences in morphology. Genetic differentiation and taxonomic status with respect to spatial distribution of 14 populations of the complex were analyzed in an effort to understand the evolution and speciation process within the genus. Allelic frequencies, levels of genetic variation, expected heterozygosity (H(S)), proportion of polymorphic loci (P), and genetic differentiation (theta and Nei's genetic distance) were estimated using 41 putative RAPD loci. All three species show high levels of genetic variation (H(S)=0.12-0.29, P=63.4-95.1), and low genetic differentiation between populations and species (theta populations=0.14+/-0.02 (SE); G(st)=0.11+/-0.02). Accordingly, gene flow among populations was estimated as high by three different methods (N(m)=2.91-6.14). Nei's genetic distances between the three species were low compared to the values obtained from other Agavaceae, and there was no clear correlation with taxonomic divisions. In a UPGMA analysis, A. subsimplex and A. cerulata formed exclusive monospecific clusters, whereas the A. deserti populations appear in more than one cluster together with other species. The results were consistent with a pattern of genetic isolation by distance.

Does experimental evolution reflect patterns in natural populations? E. coli strains from long-term studies compared with wild isolates.

Our results show that experimental evolution mimics evolution in nature. In particular, only 1,000 generations of periodic recombination with immigrant genotypes is enough for linkage disequilibrium values in experimental populations to change from a maximum linkage value to a value similar to the one observed in wild strains of E. coli. Our analysis suggests an analogy between the recombination experiment and the evolutionary history of E. coli; the E. coli genome is a patchwork of genes laterally inserted in a common backbone, and the experimental E. coli chromosome is a patchwork where some sites are highly prone to recombination and others are very clonal. In addition, we propose a population model for wild E. coli where gene flow (recombination and migration) are an important source of genetic variation, and where certain hosts act as selective sieves; i.e., the host digestive system allows only certain strains to adhere and prosper as resident strains generating a particular microbiota in each host. Therefore we suggest that the strains from a wide range of wild hosts from different regions of the world may present an ecotypic structure where adaptation to the host may play an important role in the population structure.

The elements of the locus of enterocyte effacement in human and wild mammal isolates of Escherichia coli: evolution by assemblage or disruption?

Escherichia coli is an excellent model for studying the evolution of pathogenicity since within one species various genes can be found in pathogenic islands and plasmids causing a wide spectrum of virulence. A collection of 122 strains from different human and wild mammal hosts were analysed by PCR and Southern hybridization for the presence of a subset of the genes included in the LEE (locus of enterocyte effacement). In the PCR analysis, two markers (cesT/eae and espB genes) were found together in more strains (25.4%) than either were found alone. The cesT/eae gene was less frequently found alone (8.2%) than was the espB gene (15.6%). Four regions of the LEE were analysed in a subsample of 25 strains using Southern hybridization. The four regions were all present (44%), all absent (12%) or present in different combinations (44%) in a given strain. The flanking regions of the LEE showed the highest rate of hybridization (in 72% of the strains). The results indicate that the LEE is a dynamic genetic entity, both the complete gene cluster and the individual genes. The genes that comprise this locus seem to be horizontally acquired (or lost) in an independent way and may control other functions in non-pathogenic E. coli lineages. In this way, horizontal transfer may allow the gradual stepwise construction of gene cassettes facilitating coordinate regulation and expression of novel functions.

The interaction of protein structure, selection, and recombination on the evolution of the type-1 fimbrial major subunit (fimA) from Escherichia coli.

Fimbrial adhesins allow bacteria to interact with and attach to their environment. The bacteria possibly benefit from these interactions, but all external structures including adhesins also allow bacteria to be identified by other organisms. Thus adhesion molecules might be under multiple forms of selection including selection to constrain functional interactions or evolve novel epitopes to avoid recognition. We address these issues by studying genetic diversity in the Escherichia coli type-1 fimbrial major subunit, fimA. Overall, sequence diversity in fimA is high (pi = 0.07) relative to that in other E. coli genes. High diversity is a function of positive diversifying selection, as detected by d(N)/d(S) ratios higher than 1.0, and amino acid residuces subject to diversifying selection are nonrandomly clustered on the exterior surface of the peptide. In addition, McDonald and Kreitman tests suggest that there has been historical but not current directional selection at fimA between E. coli and Salmonella. Finally, some regions of the fimA peptide appear to be under strong structural constraint within E. coli, particularly the interior regions of the molecule that is involved in subunit to subunit interaction. Recombination also plays a major role contributing to E. coli fimA allelic variation and estimates of recombination (2N(e)c) and mutation (2N(e)mu) are about the same. Recombination may act to separate the diverse evolutionary forces in different regions of the fimA peptide.

Low levels of genetic variation within and high levels of genetic differentiation among populations of species of Abies from southern Mexico and Guatemala.

Populations of Abies in southern Mexico and Guatemala (A. flinckii, A. guatemalensis, A. hickeli, and A. religiosa) have a patchy distribution. This pattern is particularly clear in A. guatemalensis. Genetic diversity within populations, measured by average heterozygosity at 16 isozyme loci, is lower than the range reported for most conifers (mean H(o) ranging from 0.069 in A. guatemalensis to 0.113 in A. flinckii), while differentiation among populations is higher than that observed in most conifer species studied (θ = F(st) ranging from 0.073 in A. hickeli to 0.271 in A. flinckii). Estimated levels of gene flow are low (ranging from 0.672 in A. flinckii to 3.17 in A. hickeli). Populations in most cases had an excess of homozygosity over that expected under Hardy-Weinberg equilibrium, suggesting some inbreeding (F(is) ranging from 0.074 in A. flinckii to 0.235 in A. guatemalensis). A significant relationship between gene flow and geographic distance was observed in A. religiosa, but not in the other three taxa studied. The patterns of genetic variation appear to have been influenced by the distributions and histories of these species. Paleoclimatic evidence suggests that the ranges of these species retreated upwards during the Pleistocene glaciation and became fragmented during the warming period that followed. The populations could have passed through genetic bottlenecks that reduced genetic variation and led to interpopulation differentiation.

Genetic diversity of the endangered endemic Agave victoriae-reginae (Agavaceae) in the Chihuahuan Desert.

Long-lived perennials are a species-rich, ecologically important component of the North American deserts, yet we know little about their genetic structure, information important for their conservation. Agave victoriae-reginae is an endemic of the Chihuahuan Desert of northern Mexico that is endangered by collection for the ornamental trade. We examined levels and patterns of variation at ten polymorphic allozyme loci in ten populations representing the range of the species. Levels of genetic variation (mean H(e)= 0.335) and differentiation (mean F(ST) = 0.236) were high. Phenetic clustering suggested the existence of at least three distinct groups of populations. If this pattern of variation is representative of other long-lived desert perennials, it may explain the species richness of this group and will pose a real challenge to gene conservation efforts.

Genetic structure of natural populations of Escherichia coli in wild hosts on different continents.

Current knowledge of genotypic and phenotypic diversity in the species Escherichia coli is based almost entirely on strains recovered from humans or zoo animals. In this study, we analyzed a collection of 202 strains obtained from 81 mammalian species representing 39 families and 14 orders in Australia and the Americas, as well as several reference strains; we also included a strain from a reptile and 10 from different families of birds collected in Mexico. The strains were characterized genotypically by multilocus enzyme electrophoresis (MLEE) and phenotypically by patterns of sugar utilization, antibiotic resistance, and plasmid profile. MLEE analysis yielded an estimated genetic diversity (H) of 0.682 for 11 loci. The observed genetic diversity in this sample is the greatest yet reported for E. coli. However, this genetic diversity is not randomly distributed; geographic effects and host taxonomic group accounted for most of the genetic differentiation. The genetic relationship among the strains showed that they are more associated by origin and host order than is expected by chance. In a dendrogram, the ancestral cluster includes primarily strains from Australia and ECOR strains from groups B and C. The most differentiated E. coli in our analysis are strains from Mexican carnivores and strains from humans, including those in the ECOR group A. The kinds and numbers of sugars utilized by the strains varied by host taxonomic group and country of origin. Strains isolated from bats were found to exploit the greatest range of sugars, while those from primates utilized the fewest. Toxins are more frequent in strains from rodents from both continents than in any other taxonomic group. Strains from Mexican wild mammals were, on average, as resistant to antibiotics as strains from humans in cities. On average, the Australian strains presented a lower antibiotic resistance than the Mexican strains. However, strains recovered from hosts in cities carried significantly more plasmids than did strains isolated from wild mammals. Previous studies have shown that natural populations of E. coli harbor an extensive genetic diversity that is organized in a limited number of clones. However, knowledge of this worldwide bacterium has been limited. Here, we suggest that the strains from a wide range of wild hosts from different regions of the world are organized in an ecotypic structure where adaptation to the host plays an important role in the population structure.

Why be a honeyless honey mesquite? Reproduction and mating system of nectarful and nectarless individuals.

Populations of Prosopis glandulosa var. torreyana in the Chihuahuan desert have a fixed dimorphic system of nectar production in which half the individuals produce nectar (are nectarful) and the other half are nectarless. We analyzed the impact of nectar production on different estimates of fitness, comparing nectarful against nectarless individuals in size, mating system, seed traits, and fruit set in a 1-ha scrubland. Of the reproductive individuals (358), 46% were nectarful and 54% were nectarless. Neither tree size nor flowering phenology differed between nectar morphs. Fixation indices (F) for both progeny (F = -0.2) and adults (F = -0.45) were negative, and high heterozygosities were found in adults and progeny (H = 0.45). No differences were found between nectar morphs for F, H, and single (t(s) = 1.1) and multilocus (t(m) = 1.03) outcrossing rates. Controlled pollinations showed differences between selfing and control treatments with no differences between nectar morphs. Nectarless individuals produced significantly more pollen grains than did nectar producers, but all other measured floral traits showed no differences. Nectarful trees were visited by pollinators 21 times more often and had a significantly higher overall fruit set than did nectarless trees. No differences between nectar morphs in seed mass or in percentage seed germination were found, but heavier seeds tended to have higher heterozygosities. Both morphs had similar success as females, but nectarless trees had ∼7% higher male function. We discuss three possible scenarios for the evolution of the fixed dimorphism in nectar production, two involving unstable phases (substitution of one morph by the other, and evolution towards dioecy) and one stable scenario (maintenance of the dimorphic system).

Isozymatic variation and phylogenetic relationships between henequen (Agave fourcroydes) and its wild ancestor A. angustifolia (Agavaceae).

Isozymatic variation and phylogenetic relationships among extant henequén (Agave fourcroydes) germplasm and wild populations of its ancestor A. angustifolia in the Yucatan Peninsula in Mexico were analyzed. Analysis of three isozyme systems using starch gel electrophoresis indicated that while A. angustifolia populations have relatively high levels of variation, within each henequén cultivar all individuals were identical. This result corresponds to previous ethnobotanical and morphological analyses, which indicated severe loss of genetic variation of this domesticated plant as a consequence of the promotion by means of asexual propagation of only one cultivar since the middle of the last century. The three extant cultivars of henequén were distinct from each other. Two of them, Sac Ki (SK) and Yaax Ki (YK), could be matched within the progenitor, but Kitam Ki (KK) has a MDH electrophenotype not found in any of the plants growing inside the Yucatan Peninsula, but found in some A. angustifolia plants growing in the Mexican states of Oaxaca and Veracruz. A parsimony analysis of the morphological data indicated two lineages: that of SK and YK, cultivated cordage plants selected for stronger and longer fibers, whose sister group is the Tropical subdeciduous forest ecotype (SF), and that of all the other wild populations, which also included KK, the cultivated textile plants selected for finer fibers and nearly extinct in Yucatan. These results support the hypothesis of the yucatecan origin of SK and YK from the SF ecotype, as well as the hypothesis of a recent introduction of KK to the Yucatan Peninsula in a domestication trend that probably included also Chelem White (its cultivation being abandoned later).

Phylogenetic analysis of rbcL sequences identifies Acorus calamus as the primal extant monocotyledon.

The identity of the oldest lineage of monocotyledons is a subject of debate. Alternative interpretations of morphological homologies are variously consistent with proposals that species of Alismatanae, Dioscoreales, or Melanthiales were the earliest descendants of the first monocotyledons. We present phylogenetic analyses based on DNA sequences of the plastid locus rbcL in which Acorus calamus, an herb with unspecialized floral features and of uncertain affinities, is supported as a member of the oldest extant lineage of monocotyledons. This conclusion is consistent with a substantial body of morphological, anatomical, and embryological evidence and offers an explanation for the failure to identify any close relationship between Acorus and other genera.