Genetic diversity and geographic pattern in early South American cotton domestication

Amplified fragment length polymorphism fingerprinting was applied to survey the genetic diversity of primitive South American Gossypium barbadense cotton for establishing a possible link to its pre-Columbian expansion. New germplasm was collected along coastal Peru and over an Andean transect in areas where most of the archaeological evidence relating to cotton domestication has been recorded. Gene bank material of three diploid (G. raimondii, G. arboreum, and G. herbaceum) and four allotetraploid cotton species (G. hirsutum, G. mustelinum, G. tomentosum and additional G. barbadense) was added for inter- and intra-specific comparison. Eight primer combinations yielded 340 polymorphic bands among the 131 accessions. The obtained neighbor joining and unweighted pair-group method with arithmetic means are in full agreement with the known cytogenetics of the tetraploid cottons and their diploid genome donors. The four tetraploid species are clearly distinct based on taxonomic classification. The genetic diversity within G. barbadense reveals geographic patterns. The locally maintained cottons from coastal Peru display a distinct genetic diversity that mirrors their primitive agro-morphological traits. Accessions from the northernmost coast of Peru and from southwestern (SW) Ecuador cluster basal to the east-of-Andes accessions. The remaining accessions from Bolivia, Brazil, Columbia, Venezuela, and the Caribbean and Pacific islands cluster with the east-of-Andes accessions. Northwestern Peru/SW Ecuador (the area flanking the Guayaquil gulf) appears to be the center of the primitive domesticated G. barbadense cotton from where it spread over the Andes and expanded into its pre-Columbian range.This publication is dedicated to Prof. Dr. Drs.h.c. Gerhard Röbbelen on the occasion of his 75th birthday     

Distribution and Differentiation of Wild,Feral, and Cultivated Populations of Perennial Upland Cotton (Gossypium hirsutum L.) in Mesoamerica and the Caribbean

Perennial forms of Gossypium hirsutum are classified under seven races. Five Mesoamerican races would have been derived from the wild race ‘yucatanense’ from northern Yucatán. ‘Marie-Galante’, the main race in the Caribbean, would have developed from introgression with G. barbadense. The racial status of coastal populations from the Caribbean has not been clearly defined. We combined Ecological Niche Modeling with an analysis of SSR marker diversity, to elucidate the relationships among cultivated, feral and wild populations of perennial cottons. Out of 954 records of occurrence in Mesoamerica and the Caribbean, 630 were classified into four categories cultivated, feral (disturbed and secondary habitats), wild/feral (protected habitats), and truly wild cotton (TWC) populations. The widely distributed three first categories cannot be differentiated on ecological grounds, indicating they mostly belong to the domesticated pool. In contrast, TWC are restricted to the driest and hottest littoral habitats, in northern Yucatán and in the Caribbean (from Venezuela to Florida), as confirmed by their climatic envelope in the factorial analysis. Extrapolating this TWC climatic model to South America and the Pacific Ocean points towards places where other wild representatives of tetraploid Gossypium species have been encountered. The genetic analysis sample comprised 42 TWC accessions from 12 sites and 68 feral accessions from 18 sites; at nine sites, wild and feral accessions were collected in close vicinity. Principal coordinate analysis, neighbor joining, and STRUCTURE consistently showed a primary divergence between TWC and feral cottons, and a secondary divergence separating ‘Marie-Galante’ from all other feral accessions. This strong genetic structure contrasts strikingly with the absence of geographic differentiation. Our results show that TWC populations of Mesoamerica and the Caribbean constitute a homogenous gene pool. Furthermore, the relatively low genetic divergence between the Mesoamerican and Caribbean domesticated pools supports the hypothesis of domestication of G. hirsutum in northern Yucatán.     

GENETIC DIVERSITY IN GOSSYPIUM HIRSUTUM AND THE ORIGIN OF UPLAND COTTON

Gossypium hirsutum has a large indigenous range encompassing most of Mesoamerica and the Caribbean, where it exhibits a diverse array of morphological forms spanning the wild-to-domesticated continuum. Modem, highly improved varieties (“Upland cotton”), which currently account for about 90% of world cotton commerce, are day-length neutral annuals derived from subtropical, perennial antecedents. To assess levels and patterns of genetic variation in the species and to elucidate the origin of Upland cotton, 538 accessions representing the full spectrum of morphological and geographical diversity were analyzed forallozyme variation at 50 loci. Levels of variation are modest overall but are low in Upland cotton. Relationships among accessions reflect pre-Columbian influences of aboriginal peoples and later European colonists superimposed on the preagricultural pattern. In contrast to expectations, two centers of diversity are evident, one in southern Mexico-Guatemala and the other in the Caribbean. Introgression of G. barbadense genes into G. hirsutum has been common in a broad area of sympatry in the Caribbean. The germplasm of present cultivars traces to Mexican highland stocks, which, in turn, were derived from material originally from southern Mexico and Guatemala. Despite the widespread belief that germplasm from several other species has been incorporated into modem Upland stocks through intentional breeding efforts, the 50 Upland cultivars examined contain no unique alleles, suggesting that retention of genes from transspecific sources has been minimal. The most recent infraspecific treatment, which recognizes seven races, does not adequately represent genetic relationships.     

Some observations on photoperiodism and the development of annual forms of domesticated cottons

Observations made over the last fifteen to twenty years have discovered no primitive forms of G.barbadense L. orG. hirsutum L. (other than G.hirsutum racelatifolium Hutchinson) which are capable of flowering during the long summer days of temperate latitudes. Annual Upland cottons, grown in the southern United States since the mid-eighteenth century, were probably derived from perennial day-neutral forms of Mexican racelatifolium, though not necessarily by direct introduction from Mexico into the United States. The origin of Sea Island cottons (day-neutral forms of G.barbadense), which were formerly grown on the southeastern seaboard of the United States since the mid-eighteenth century, remains obscure. No primitive forms of this species, capable of flowering during the long summer days of temperate latitudes, have been found. An experiment is reported in which it has been possible to synthesize a day-neutral form of G.barbadense through introgression between primitive short-day sensitive forms of G.barbadense and G.hirsutum, both native to the Caribbean region. It is suggested that the ancestors of Sea Island cottons may have originated naturally by a similar mechanism involving the same species.     

Bidirectional cytoplasmic and nuclear introgression in the New World cottons Gossypium barbadense and G. Hirsutum (Malvaceae)

Patterns of interspecific cytoplasmic (plastid and mitochondrial) and nuclear introgression are typically asymmetrical: cytoplasmic gene flow or “capture” is frequently observed without evidence of nuclear introgression. In contrast, nuclear introgression without concomitant cytoplasmic introgression has rarely been demonstrated. Gossypium barbadense L. and G. hirsutum L. have large indigenous ranges in the New World semiarid tropics, with an extensive area of sympatry in the Caribbean and Central America. Numerous accessions of both species were surveyed for diagnostic cpDNA restriction sites. These data, in conjunction with previous information on nuclear markers, lead to several conclusions: 1) introgression between G. hirsutum and G. barbadense is bidirectional for both nuclear and cytoplasmic genes; 2) patterns of introgression between the two species are not symmetrical—in G. barbadense, introgression of G. hirsutum alleles is largely restricted to modem cultivars and is uncommon in areas of sympatry; in contrast, introgression of G. barbadense alleles into G. hirsutum is relatively common in areas of sympatry and is rare in modem cultivars; 3) nuclear introgression is geographically more widespread and more frequently detected than cytoplasmic introgression. Several mechanisms may underlie the differential patterns of cytoplasmic and nuclear gene flow observed, including differential fitness of infraspecific and interspecific cytonuclear combinations and selection against female function in interspecific backcrosses. Possible explanations for the observed asymmetrical patterns of introgression include differences in population sizes combined with phenological differences that bias interspecific pollen transfer.     

A tale of two haplotype groups: evaluating the New World Junonia ring species hypothesis using the distribution of divergent COI haplotypes

The New World Junonia butterflies are a possible ring species with a circum‐Caribbean distribution. Previous reports suggest a steady transition between North and South American forms in Mesoamerica, but in Cuba the forms were thought to co‐exist without interbreeding representing the overlapping ends of the ring. Three criteria establish the existence of a ring species: a ring‐shaped geographic distribution, gene flow among intervening forms and genetic isolation in the region of range overlap. We evaluated mitochondrial cytochrome oxidase I haplotypes in Junonia from nine species in the Western Hemisphere to test the Junonia ring species hypothesis. Junonia species are generally not monophyletic with respect to COI haplotypes, which are shared across species. However, two major COI haplotype groups exist. Group A predominates in South America, and Group B predominates in North and Central America. Therefore, COI haplotypes can be used to assess the degree of genetic influence a population receives from each continent. Junonia shows a ring‐shaped distribution around the Caribbean, and evidence is consistent with gene flow among forms of Junonia, including those from Mesoamerica. However, we detected no discontinuity in gene flow in Cuba or elsewhere in the Caribbean consistent with genetic isolation in the region of overlap. Although sampling is still very limited in the critical region, the only remaining possibility for a circum‐Caribbean discontinuity in gene flow is at the Isthmus of Panama, where there may be a transition from 98% Group B haplotypes in Costa Rica to 85–100% Group A haplotypes in South America.     

Molecular phylogeny supports a Northern Hemisphere origin of Golovinomyces (Ascomycota: Erysiphales)

Golovinomyces is a strictly herb-parasitic genus in the Erysiphaceae. Host–parasite co-speciation was reported recently between the genus Golovinomyces and Asteraceae from molecular phylogenetic analyses. The Asteraceae originated in South America and latterly expanded their geographic distribution into the Northern Hemisphere. If the co-speciation between Golovinomyces and Asteraceae originated in South America, the geographic origin of Golovinomyces could be assumed to be South America. To address this question, Golovinomyces species from hosts of the tribe Mutisieae, an asteraceous tribe endemic to South America, were collected and the ITS and 28S rDNA regions sequenced. Results indicate that Oidium mutisiae and Golovinomyces leuceriae isolated from the Mutisieae do not belong at the base of the Golovinomyces tree. Instead, they are situated separately within two different clades of Golovinomyces isolates from the Northern Hemisphere. Therefore, the tribe Mutisieae is not the most early host of Golovinomyces. Present results suggest that Golovinomyces originated in the Northern Hemisphere, and not in South America. The new species Oidium reginae for the previous O. mutisiae on Mutisia decurrens is proposed.     

Diversification of Lupinus (Leguminosae) in the western New World: derived evolution of perennial life history and colonization of montane habitats

Previous phylogenetic studies of Lupinus (Leguminosae) based on nuclear DNA have shown that the western New World taxa form a monophyletic group representing the majority of species in the genus, with evidence for high rates of recent diversification in South America following final uplift of the Andes 2–4 million years ago (Mya). For this study, three regions of rapidly evolving non-coding chloroplast DNA (trnL intron, trnS–trnG, and trnT–trnL) were examined to estimate the timing and rates of diversification in the western New World, and to infer ancestral states for geographic range, life history, and maximum elevation. The western New World species (5.0–9.3 Mya, 0.6–1.1 spp./My) comprise a basally branching assemblage of annual plants endemic to the lower elevations of western North America, from which two species-rich clades are recently derived: (i) the western North American perennials from the Rocky Mountains, Great Basin, and Pacific Slope (0.7–2.1 Mya, 2.0–5.9 spp./My) and (ii) the predominantly perennial species from the Andes Mountains of South America and highlands of Mexico (0.8–3.4 Mya, 1.4–5.7 spp./My). Bayesian posterior predictive tests for association between life history and maximum elevation demonstrate that perennials are positively correlated with higher elevations. These results are consistent with a series of one or more recent radiations in the western New World, and indicate that rapid diversification of Lupinus coincides with the derived evolution of perennial life history, colonization of montane habitats, and range expansion from North America to South America.     

Potential Global Range Expansion of the Invasive Fire Ant, Solenopsis invicta

The red imported fire ant, Solenopsis invicta Buren, is an invasive pest that has become widespread in the southern United States and Caribbean after introduction from South America in the 1930s. This species, which has diverse detrimental impacts on recipient communities, was recently discovered in Australia and New Zealand and has the potential to colonize numerous other regions. We used a dynamic, ecophysiological model of colony growth to predict the potential global range expansion of this invasive species. Based on minimum and maximum daily temperatures, the model estimates colony alate production and predicts future geographic range limits. Because S. invicta populations are limited by arid conditions as well as cold temperatures, we superimposed precipitation data upon temperature-based predictions, to identify regions that do not receive enough rainfall to support this species across the landscape. Many areas around the globe, including large portions of Europe, Asia, Africa, Australia, and numerous island nations, are at risk for S. invicta infestation. Quarantine officials should be vigilant for any accidental introductions of this pest in susceptible regions. Costs of eradication increase dramatically as the area of infestation grows, and large infestations may be impossible to eradicate. Other South American Solenopsis fire ants (e.g., S. richteri Forel) may become invasive if the opportunity arises, and our predictions for S. invicta may approximate the potential range limits for these species as well.     

斑纹小贻贝(Mytella strigata)基础生物学与生物入侵

生物入侵是继栖息地破坏之后,全球生物多样性丧失的第二大驱动因素。近年来,原产于南美洲地区的斑纹小贻贝（Mytella strigata）在印度-西太平洋海区被陆续报道,而我国台湾、广东、海南、福建、广西等省份同样发现斑纹小贻贝,且其已经建立可自我维持的种群。但是,作为一种新型入侵生物,斑纹小贻贝尚未引起国内海洋管理部门和科研人员足够重视,亟待查明其在我国沿海的分布现状、扩散趋势和生态影响等,为斑纹小贻贝的检测、监测、防控和管理提供科学依据。综述了斑纹小贻贝的基础生物学特征和全球生物入侵现状,发现国内的斑纹小贻贝源于南美洲加勒比海地区,于2014年左右通过船舶压舱水或船体生物污损的形式侵入我国南方沿海并迅速扩散。此外,斑纹小贻贝在我国的生物入侵处于"引进-传播"阶段,即将大规模扩繁,因此亟需开展应急清除行动。     

Restriction fragment length polymorphism analysis of CCDD genome species of the genus Oryza L.

Restriction fragment length polymorphisms (RFLPs) were studied in fourteen accessions of CCDD genome allotetraploid wild rice species (Oryza latifolia, O. alta and O. grandiglumis). Fourteen nuclear RFLP markers previously mapped in AA genome-cultivated rice were used as probes. A phylogenetic tree, constructed by parsimony analysis based on RFLPs, grouped the accessions according to their geographic origin from Central or South America. Oryza alta, O. grandiglumis and one accession of O. latifolia grouped together as a subgroup, and our results suggested that the three taxa should be considered as populations of a single complex species. Duplicate loci, representing the two constituent genomes of the allotetraploid, were observed for most RFLP markers. By comparing RFLPs from the allotetraploids with those from a CC genome diploid wild species (O. officinalis), it was possible to detect RFLPs specific for both the CC and DD genomes of the allotetraploid. In inter-accession F2 populations, independent segregation of RFLP markers for CC and DD genomes was observed.     

Microsatellite diversity in tetraploid <Emphasis Type="Italic">Gossypium</Emphasis> germplasm: assembling a highly informative genotyping set of cotton SSRs

A series of 320 mapped simple sequence repeats (SSRs) have been used to screen the allelic diversity of tetraploid Gossypium species. Fourty-seven genotypes were analyzed representing (i) the wide spectrum of diversity of the cultivated pool and of the primitive landraces of species G. hirsutum (‘marie-galante’, ‘punctatum’, ‘richmondi’, ‘morrilli’, ‘palmeri’, and ‘latifolium’, and ‘yucatanense’), and (ii) species G. barbadense, G. darwinii and G. tomentosum. The polymorphism of 201 SSR loci revealed 1128 allelic variants ranging from 3 to 17 per locus. Neighbor-joining (NJ) method based on genetic dissimilarities produced groupings consistent with the assignments of accessions both at species and at race level. Our data confirmed the proximity of the Galapagos endemic species G. darwinii to species G. barbadense. Within species G. hirsutum, and as compared to the other 6 races, race yucatanense appeared as the most distant from cultivated genotypes. Race yucatanense also exhibited the highest number of unique alleles. The important informative heterogeneity of the 201 SSR loci was exploited to select the most polymorphic ones that were assembled into three series of genome-wide (i.e. each homoeologous AD chromosome pair being equally represented) and mutliplexable (× 3) SSRs. Using one of these ‘genotyping set’, consisting of 39 SSRs (one 3-plex for each of the 13 AD chromosomes pairs) or 45 loci, we were able to assess the relationships between accessions and the topology in the genetic diversity sampled. Such genotyping set of highly informative SSR markers assembled in PCR-multiplex, while increasing genotyping throughput, will be applicable for molecular genetic diversity studies of large germplasm collections. Electronic Supplementary Material Supplementary material is available in the online version of this article at and is accessible for authorized users.     

Dispersal barriers and climate determine the geographic distribution of the helicopter damselfly Mecistogaster modesta

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2C DNA variation and relationships among New World species of the genus Lupinus (Fabaceae)

The 2C DNA values in 38 species and accessions of the genus Lupinus (Fabaceae) from the New World have been analysed using flow cytometry. They are representatives of North and South American species (the Atlantic and the Andean regions). Estimated 2C DNA values ranged from 1.08 pg in L. pusillus to 2.68 pg in L. albicaulis (both from North America), that is a variation of more than 2.5-fold. The variation for North American lupins was much higher than that for South American ones. Statistical analysis of the data resulted in a grouping that showed for North American lupins some correlation with the length of life cycle. Discussion concerns some aspects of the evolution of the genus.     

Geographical distributions of spiny pocket mice in South America: insights from predictive models

Aim Predictive models of species’ distributions use occurrence records and environmental data to produce a model of the species’ requirements and a map of its potential distribution. To determine regions of suitable environmental conditions and assess biogeographical questions regarding their ranges, we modelled the potential geographical distributions of two spiny pocket mice (Rodentia: Heteromyidae) in north‐western South America. Location North‐western South America. Methods We used the Genetic Algorithm for Rule‐Set Prediction (GARP), environmental data from GIS maps and georeferenced collection localities from a recent systematic review of Heteromys australis and H. anomalus to produce the models. Results GARP models indicate the potential presence of H. australis throughout mesic montane regions of north‐western South America, as well as in some lowland regions of moderately high precipitation. In contrast, H. anomalus is predicted to occur primarily in drier areas of the Caribbean coast and rain‐shadowed valleys of the Andes. Conclusions The models support the disjunct status of the population of H. australis in the Cordillera de Mérida, but predict a continuous distribution between known populations of H. anomalus in the upper Magdalena Valley and the Caribbean coast. Regions of suitable environmental conditions exist disjunct from known distributional areas for both species, suggesting possible historical restrictions to their ranges. This technique holds wide application to other study systems.     

The island cotton NBS‐LRR gene GbaNA1 confers resistance to the non‐race 1 Verticillium dahliae isolate Vd991

Wilt caused by Verticillium dahliae significantly reduces cotton yields, as host resistance in commercially cultivated Gossypium species is lacking. Understanding the molecular basis of disease resistance in non‐commercial Gossypium species could galvanize the development of Verticillium wilt resistance in cultivated species. Nucleotide‐binding site leucine‐rich repeat (NBS‐LRR) proteins play a central role in plant defence against pathogens. In this study, we focused on the relationship between a locus enriched with eight NBS‐LRR genes and Verticillium wilt resistance in G. barbadense. Independent virus‐induced gene silencing of each of the eight NBS‐LRR genes in G. barbadense cultivar Hai 7124 revealed that silencing of GbaNA1 alone compromised the resistance of G. barbadense to V. dahliae isolate Vd991. In cultivar Hai 7124, GbaNA1 could be induced by V. dahliae isolate Vd991 and by ethylene, jasmonic acid and salicylic acid. Nuclear protein localization of GbaNA1 was demonstrated by transient expression. Sequencing of the GbaNA1 orthologue in nine G. hirsutum accessions revealed that all carried a non‐functional allele, caused by a premature peptide truncation. In addition, all 10 G. barbadense and nine G. hirsutum accessions tested carried a full‐length (～1140 amino acids) homologue of the V. dahliae race 1 resistance gene Gbve1, although some sequence polymorphisms were observed. Verticillium dahliae Vd991 is a non‐race 1 isolate that lacks the Ave1 gene. Thus, the resistance imparted by GbaNA1 appears to be mediated by a mechanism distinct from recognition of the fungal effector Ave1.     

Inter-Specific Differences in Cotton for Nutrient Partitioning from Subtending Leaves to Reproductive Parts at Various Developmental Stages: Consequences for Fruit Growth and Yield

A field study was carried out to unravel the inter-specific differences in cotton for the partitioning of N, P, K, S, Ca, Mg, Na and Cl from the subtending leaves to the reproductive parts of Gossypium hirsutum, G. barbadense and G. arboreum at various developmental stages. Results revealed significant differences among the species for the various parameters studied. Overall there was a greater fresh and dry matter yield of various reproductive parts and subtending leaves of G. hirsutum and G. barbadense than G. arboreum, although the leaf photosynthetic rate was similar. Age-dependent increase in leaf area/leaf mass ratio indicated a greater partitioning of earlier acquired assimilates to the growth of reproductive parts. Results indicated greater partitioning of N, P, S and Ca during later reproductive growth (from boll production to its opening) in G. hirsutum and G. barbadense but during earlier reproductive growth in G. arboreum (from bud up to flower formation) as was evident by decreased subtending leaf/reproductive parts ratio. It is concluded that better N, P, S and Ca partitioning ability of G. hirsutum and G. barbadense at the onset of boll development played a major role in the better yield and good quality fiber characteristics. This revised version was published online in July 2006 with corrections to the Cover Date.     

Oral yeast flora and its ITS sequence diversity among a large cohort of medical students in Hainan,China

The most prevalent fungal infection of humans is candidiasis which is caused by species of Candida that are typical members of the commensal microbial flora of the oral mucosa and other body surfaces. Since species of Candida differ in virulence properties and susceptibilities to anti-fungal drugs, understanding the human commensal yeast flora will have a significant impact on designing treatment and prevention strategies against yeast infections. However, although there is a global interest in Candida species, the global distributions of Candida species remain largely unknown, especially among healthy hosts. Here we report the oral yeast flora from the surveys of over 1,000 medical students in China. Our results showed that this population had a yeast carriage rate (4.5%) much lower than other population samples reported previously from Mainland China (40–70%). In addition, C. albicans was isolated at a much higher frequency than those from other Chinese samples, with a frequency (80.9%) more similar to those in developed regions such as North America. The oral yeast carriage rates and yeast species compositions were similar between male and female students and between the hosts borne and raised on Hainan Island and those borne and raised on Mainland China. Furthermore, the sequence variation at the internal transcribed spacer (ITS) regions of the nuclear ribosomal RNA gene cluster was analyzed for strains of the dominant species, C. albicans. Our analysis identified 14 ITS types among the 41 Hainan isolates of C. albicans. However, only four of the 14 ITS types were identical to those in reference strains from Europe and North America. Taken together, our analyses suggest that the oral yeast flora among host populations in China is highly heterogeneous and that there is a high ITS sequence diversity in the Hainan population of C. albicans.     

Interrelationship of cultivated rices Oryza sativa and O. glaberrima with wild O. perennis complex

Summary Phylogenetic relationship of the cultivated rices Oryza sativa and O. glaberrima with the O. perennis complex, distributed on the three continents of Asia, Africa and America, and O. australiensis has been studied using Fraction 1 protein and two repeated DNA sequences as markers. Fraction 1 protein isolated from the leaf tissue of accessions of different species was subjected to isoelectric focusing. All the species studied have similar nuclear-encoded small subunit polypeptides and chloroplast-encoded large subunit polypeptides, except two of the O. perennis accessions from South America and O. australiensis, which have a different pattern for the chloroplast subunit. Two DNA sequences were isolated from Eco R1 restriction endonuclease digests of total DNA from O. sativa. One of the sequences has been characterized as highly repeated satellite DNA, and the other one as a moderately repeated DNA sequence. These sequences were used as probes in DNA/DNA hybridization with restriction endonuclease digested DNA from some accessions of the different species. Those accessions that are divergent for large subunit polypeptides of Fraction 1 protein (O. australiensis and two of the four South American O. perennis accessions) also lack the satellite DNA and have a different hybridization pattern with the moderately repeated sequence. All other accessions, irrespective of their geographical origin, are similar. We propose that various accessions of O. perennis from Africa and Asia are closely related to O. sativa and O. glaberrima, and that the dispersal of cultivated and O. perennis rices to different continents may be quite recent. The American O. perennis is a heterogeneous group. Some of the accessions ascribed to this group are closely related to the Asian and African O. perennis, while others have diverged.