Almost forgotten or latest practice? AFLP applications, analyses and advances

Short Tandem Repeat Genotyping of Medically Important Fungi: A Comprehensive Review of a Powerful Tool with Extensive Future Potential

Fungal infections pose an increasing threat to public health. New pathogens and changing epidemiology are a pronounced risk for nosocomial outbreaks. To investigate clonal transmission between patients and trace the source, genotyping is required. In the last decades, various typing assays have been developed and applied to different medically important fungal species. While these different typing methods will be briefly discussed, this review will focus on the development and application of short tandem repeat (STR) genotyping. This method relies on the amplification and comparison of highly variable STR markers between isolates. For most common fungal pathogens, STR schemes were developed and compared to other methods, like multilocus sequence typing (MLST), amplified fragment length polymorphism (AFLP) and whole genome sequencing (WGS) single nucleotide polymorphism (SNP) analysis. The pros and cons of STR typing as compared to the other methods are discussed, as well as the requirements for the development of a solid STR typing assay. The resolution of STR typing, in general, is higher than MLST and AFLP, with WGS SNP analysis being the gold standard when it comes to resolution. Although most modern laboratories are capable to perform STR typing, little progress has been made to standardize typing schemes. Allelic ladders, as developed for Aspergillus fumigatus, facilitate the comparison of STR results between laboratories and develop global typing databases. Overall, STR genotyping is an extremely powerful tool, often complimentary to whole genome sequencing. Crucial details for STR assay development, its applications and merit are discussed in this review.

In vitro virulotyping, antifungal susceptibility testing and DNA fingerprinting of Microsporum canis strains of canine and feline origin

Microsporum canis is considered the common dermatophyte agent associated with ringworm in felines and canines. In the present study, we sampled n = 548 felines and canines for the probable isolation of M. canis. The rate of isolation from the cats and dogs was 70.27 % (52/74) and 1.68 % (8/474), respectively and Persian cats were found to be highly susceptible to M. canis infection. The strains were evaluated for their production of phospholipase, lipase, catalase, and hemolysis and their ability to grow at 35 ℃. All the strains were identified as low producers of catalase and n = 17 strains exhibited high thermotolerance ability. Terbinafine was found to be the most effective antifungal drug and fluconazole was the least effective, in vitro. AFLP analysis revealed three genotypes of M. canis with 15 sub-clusters showing ≥ 90 % similarity and 7 sub-clusters exhibiting 100 % similarity. However, the phenotypic characters cannot be attributed based on the AFLP profiles.

Allopolyploidy: An Underestimated Driver in Juniperus Evolution

Allopolyploidy is considered as a principal driver that shaped angiosperms' evolution in terms of diversification and speciation. Despite the unexpected high frequency of polyploidy that was recently discovered in the coniferous genus Juniperus, little is known about the origin of these polyploid taxa. Here, we conducted the first study devoted to deciphering the origin of the only hexaploid taxon in Juniperus along with four of its closely related tetraploid taxa using AFLP markers with four primers combinations. Phylogenetic analysis revealed that the 10 studied species belong to 2 major clusters. J. foetidissima appeared to be more related to J. thurifera, J. sabina, and J. chinensis. The Bayesian clustering analysis showing a slight variation in genetic admixture between the studied populations of J. foetidissima, suggesting an allopolyploid origin of this species involving J. thurifera and J. sabina lineages, although a purely autopolyploidy origin of both J. thurifera and J. foetidissima cannot be ruled out. The admixed genetic pattern revealed for J. seravschanica showed that the tetraploid cytotypes of this species originated from allopolyploidy, whereas no clear evidence of hybridization in the origin of the tetraploid J. thurifera and J. chinensis was detected. This study provides first insights into the polyploidy origin of the Sabina section and highlights the potential implication of allopolyploidy in the evolution of the genus Juniperus. Further analyses are needed for a more in-depth understanding of the evolutionary scenarios that produced the observed genetic patterns.

Vitis vinifera genotyping toolbox to highlight diversity and germplasm identification

The contribution of vine cultivation to human welfare as well as the stimulation of basic social and cultural features of civilization has been great. The wide temporal and regional distribution created a wide array of genetic variants that have been used as propagating material to promote cultivation. Information on the origin and relationships among cultivars is of great interest from a phylogenetics and biotechnology perspective. Fingerprinting and exploration of the complicated genetic background of varieties may contribute to future breeding programs. In this review, we present the most frequently used molecular markers, which have been used on Vitis germplasm. We discuss the scientific progress that led to the new strategies being implemented utilizing state-of-the-art next generation sequencing technologies. Additionally, we attempted to delimit the discussion on the algorithms used in phylogenetic analyses and differentiation of grape varieties. Lastly, the contribution of epigenetics is highlighted to tackle future roadmaps for breeding and exploitation of Vitis germplasm. The latter will remain in the top of the edge for future breeding and cultivation and the molecular tools presented herein, will serve as a reference point in the challenging years to come.

Applying molecular and genetic methods to trees and their fungal communities

Forests provide invaluable economic, ecological, and social services. At the same time, they are exposed to several threats, such as fragmentation, changing climatic conditions, or increasingly destructive pests and pathogens. Trees, the inherent species of forests, cannot be viewed as isolated organisms. Manifold (micro)organisms are associated with trees playing a pivotal role in forest ecosystems. Of these organisms, fungi may have the greatest impact on the life of trees. A multitude of molecular and genetic methods are now available to investigate tree species and their associated organisms. Due to their smaller genome sizes compared to tree species, whole genomes of different fungi are routinely compared. Such studies have only recently started in forest tree species. Here, we summarize the application of molecular and genetic methods in forest conservation genetics, tree breeding, and association genetics as well as for the investigation of fungal communities and their interrelated ecological functions. These techniques provide valuable insights into the molecular basis of adaptive traits, the impacts of forest management, and changing environmental conditions on tree species and fungal communities and can enhance tree-breeding cycles due to reduced time for field testing. It becomes clear that there are multifaceted interactions among microbial species as well as between these organisms and trees. We demonstrate the versatility of the different approaches based on case studies on trees and fungi. KEY POINTS: • Current knowledge of genetic methods applied to forest trees and associated fungi. • Genomic methods are essential in conservation, breeding, management, and research. • Important role of phytobiomes for trees and their ecosystems.

Asexually propagated Agave tequilana var. azul exhibits variation in genetic markers and defence responses to Fusarium solani

Agave (Agave tequilana var. azul) is considered a crop with low genetic diversity because it has been propagated vegetatively for centuries for commercial purposes, and consequently, it could be equally susceptible to pests and diseases. However, the present study employs plant material derived from field-grown plants exhibiting phenotypic variability in susceptibility to agave wilt. The offshoots from rhizomes of these plants were reproduced in vitro and classified as potentially resistant or susceptible. Amplified fragment length polymorphism analysis confirmed wide genetic differences among individuals, but these differences were not correlated with the observed phenotypic variability in resistance. Propagated plantlets were inoculated with Fusarium solani in two time-lapse confrontations for 72 h and 30 days. The early biochemical response showed statistically superior levels in the accumulation of shikimic acid, phenolic compounds, and chitinase activity in potentially resistant plantlets. There was an inverse correlation of these early biochemical responses and salicylic acid and the incidence of diseased root cells in isogenic plantlets in the 30-day confrontation with F. solani, suggesting that these activities and accumulation of molecules were primordial in the defence against this pathogen.

The conservation and ecology of the British Virgin Islands endemic tree, Vachellia anegadensis

Numerous island species have gone extinct and many extant, but threatened, island endemics require ongoing monitoring of their conservation status. The small tree Vachellia anegadensis was formerly thought to occur only on the limestone island of Anegada in the British Virgin Islands and was categorized as Critically Endangered. However, in 2008 it was discovered on the volcanic island of Fallen Jerusalem, c. 35 km from Anegada, and in 2018 it was recategorized as Endangered. To inform conservation interventions, we examined the species’ distribution, genetic population structure, dependency on pollinators and preferred habitat, and documented any threats. We found V. anegadensis to be locally widespread on Anegada but uncommon on Fallen Jerusalem and established that geographical location does not predict genetic differentiation amongst populations. Vachellia anegadensis produces the highest number of seed pods when visited by animal pollinators, in particular Lepidoptera. Introduced animals and disturbance by humans appear to be the main threats to V. anegadensis, and in situ conservation is critical for the species’ long-term survival.

Performance comparison of two reduced-representation based genome-wide marker-discovery strategies in a multi-taxon phylogeographic framework

Multi-locus genetic data are pivotal in phylogenetics. Today, high-throughput sequencing (HTS) allows scientists to generate an unprecedented amount of such data from any organism. However, HTS is resource intense and may not be accessible to wide parts of the scientific community. In phylogeography, the use of HTS has concentrated on a few taxonomic groups, and the amount of data used to resolve a phylogeographic pattern often seems arbitrary. We explore the performance of two genetic marker sampling strategies and the effect of marker quantity in a comparative phylogeographic framework focusing on six species (arthropods and plants). The same analyses were applied to data inferred from amplified fragment length polymorphism fingerprinting (AFLP), a cheap, non-HTS based technique that is able to straightforwardly produce several hundred markers, and from restriction site associated DNA sequencing (RADseq), a more expensive, HTS-based technique that produces thousands of single nucleotide polymorphisms. We show that in four of six study species, AFLP leads to results comparable with those of RADseq. While we do not aim to contest the advantages of HTS techniques, we also show that AFLP is a robust technique to delimit evolutionary entities in both plants and animals. The demonstrated similarity of results from the two techniques also strengthens biological conclusions that were based on AFLP data in the past, an important finding given the wide utilization of AFLP over the last decades. We emphasize that whenever the delimitation of evolutionary entities is the central goal, as it is in many fields of biodiversity research, AFLP is still an adequate technique.

Population Genetics of Odontarrhena (Brassicaceae) from Albania: The Effects of Anthropic Habitat Disturbance, Soil, and Altitude on a Ni-Hyperaccumulator Plant Group from a Major Serpentine Hotspot

Albanian taxa and populations of the genus Odontarrhena are most promising candidates for research on metal tolerance and Ni-agromining, but their genetic structure remains unknown. We investigated phylogenetic relationships and genetic differentiation in relation to distribution and ploidy of the taxa, anthropic site disturbance, elevation, soil type, and trace metals at each population site. After performing DNA sequencing of selected accessions, we applied DNA-fingerprinting to analyze the genetic structure of 32 populations from ultramafic and non-ultramafic outcrops across Albania. Low sequence divergence resulted in poorly resolved phylograms, but supported affinity between the two diploid serpentine endemics O. moravensis and O. rigida. Analysis of molecular variance (AMOVA) revealed significant population differentiation, but no isolation by distance. Among-population variation was higher in polyploids than in diploids, in which genetic distances were lower. Genetic admixing at population and individual level occurred especially in the polyploids O. chalcidica, O. decipiens, and O. smolikana. Admixing increased with site disturbance. Outlier loci were higher in serpentine populations but decreased along altitude with lower drought and heat stress. Genetic variability gained by gene flow and hybridization at contact zones with "resident" species of primary ultramafic habitats promoted expansion of the tetraploid O. chalcidica across anthropogenic sites.

Vegetation growth and landscape genetics of Tillandsia lomas at their dry limits in the Atacama Desert show fine-scale response to environmental parameters

Ecosystem dry limits have been studied in the context of species biology, fitness, and interactions with biotic and abiotic parameters, but the interactive effects of these parameters remain underexplored. Therefore, information on the putative effects of global climate change on these ecosystems is often lacking.We analyzed the interplay between fine-scale landscape genetics and biotic and abiotic factors of terrestrial Tillandsia lomas in the hyperarid Atacama Desert, characterized by a fog-dependent vegetation type almost entirely dominated by one single vascular plant species.We showed that metapopulations of Tillandsia landbeckii are genetically connected over many hundreds of square kilometers, and despite having a large potential for clonal propagation, genetic diversity is regionally and locally structured. At the landscape level, genetic diversity correlates well with fitness parameters such as growth, flowering, and vegetation density. We also observed fine-scale correlation with a 3-D landscape model indicating a positive feedback with seasonal fog occurrence and availability. The various interactions of biotic and abiotic factors resulted in regular linear banding patterns of vegetation arranged orthogonally toward the landscape slope. Ex situ growth experiments indicated that T. landbeckii grows at optimal rates in this extreme hyperarid environment, and we can extrapolate mean biomass production for this ecosystem. Synthesis. Our results suggest that the unique ecosystem of terrestrial Tillandsia lomas in the hyperarid Atacama Desert is an evolutionarily balanced and fine-scaled system. The vegetation itself is composed of long-lived and persistent modules. We developed a descriptive model of the various interacting factors, thereby also highlighting the severe threat caused by global climate change potentially associated with fog disturbance patterns along the Chilean Pacific coast.

Ecology and Genetic Structure of the Parasitoid Phobocampe confusa (Hymenoptera: Ichneumonidae) in Relation to Its Hosts, Aglais Species (Lepidoptera: Nymphalidae)

The biology of parasitoids in natural ecosystems remains very poorly studied, though they are key species for their functioning. Here we focused on Phobocampe confusa, a Nymphalini specialist, responsible for high mortality rates in charismatic butterfly species in Europe (genus Aglais). We studied its ecology and genetic structure in connection with those of its host butterflies in Sweden. To this aim, we gathered data from 428 P. confusa individuals reared from 6094 butterfly larvae (of A. urticae, A. io, and in two occasions of Araschnia levana) collected over two years (2017 and 2018) and across 19 sites distributed along a 500 km latitudinal gradient. We found that P. confusa is widely distributed along the latitudinal gradient. Its distribution seems constrained over time by the phenology of its hosts. The large variation in climatic conditions between sampling years explains the decrease in phenological overlap between P. confusa and its hosts in 2018 and the 33.5% decrease in the number of butterfly larvae infected. At least in this study, P. confusa seems to favour A. urticae as host. While it parasitized nests of A. urticae and A. io equally, the proportion of larvae parasitized is significantly higher for A. urticae. At the landscape scale, P. confusa is almost exclusively found in vegetated open land and near deciduous forests, whereas artificial habitats are negatively correlated with the likelihood of a nest to be parasitized. The genetic analyses on 89 adult P. confusa and 87 adult A. urticae using CO1 and AFLP markers reveal a low genetic diversity in P. confusa and a lack of genetic structure in both species, at the scale of our sampling. Further genetic studies using high-resolution genomics tools will be required to better understand the population genetic structure of P. confusa, its biotic interactions with its hosts, and ultimately the stability and the functioning of natural ecosystems.

The Quaternary evolutionary history of Bristol rock cress (Arabis scabra, Brassicaceae), a Mediterranean element with an outpost in the north-western Atlantic region

BACKGROUND AND AIMS

Bristol rock cress is among the few plant species in the British Isles considered to have a Mediterranean-montane element. Spatiotemporal patterns of colonization of the British Isles since the last interglacial and after the Last Glacial Maximum (LGM) from mainland Europe are underexplored and have not yet included such floristic elements. Here we shed light on the evolutionary history of a relic and outpost metapopulation of Bristol rock cress in the south-western UK.

METHODS

Amplified fragment length polymorphisms (AFLPs) were used to identify distinct gene pools. Plastome assembly and respective phylogenetic analysis revealed the temporal context. Herbarium material was largely used to exemplify the value of collections to obtain a representative sampling covering the entire distribution range.

KEY RESULTS

The AFLPs recognized two distinct gene pools, with the Iberian Peninsula as the primary centre of genetic diversity and the origin of lineages expanding before and after the LGM towards mountain areas in France and Switzerland. No present-day lineages are older than 51 ky, which is in sharp contrast to the species stem group age of nearly 2 My, indicating severe extinction and bottlenecks throughout the Pleistocene. The British Isles were colonized after the LGM and feature high genetic diversity.

CONCLUSIONS

The short-lived perennial herb Arabis scabra, which is restricted to limestone, has expanded its distribution range after the LGM, following corridors within an open landscape, and may have reached the British Isles via the desiccated Celtic Sea at about 16 kya. This study may shed light on the origin of other rare and peculiar species co-occurring in limestone regions in the south-western British Isles.

Comparative genetic and epigenetic diversity in pairs of sympatric, closely related plants with contrasting distribution ranges in south-eastern Iberian mountains

Genetic diversity defines the evolutionary potential of a species, yet mounting evidence suggests that epigenetic diversity could also contribute to adaptation. Elucidating the complex interplay between genetic and epigenetic variation in wild populations remains a challenge for evolutionary biologists, and the intriguing possibility that epigenetic diversity could compensate for the loss of genetic diversity is one aspect that remains basically unexplored in wild plants. This hypothesis is addressed in this paper by comparing the extent and patterns of genetic and epigenetic diversity of phylogenetically closely related but ecologically disparate species. Seven pairs of congeneric species from Cazorla mountains in south-eastern Spain were studied, each pair consisting of one endemic, restricted-range species associated to stressful environments, and one widespread species occupying more favourable habitats. The prediction was tested that endemic species should have lower genetic diversity due to population fragmentation, and higher epigenetic diversity induced by environmental stress, than their widespread congeners. Genetic (DNA sequence variants) and epigenetic (DNA cytosine methylation variants) diversities and their possible co-variation were assessed in three populations of each focal species using amplified fragment length polymorphism (AFLP) and methylation-sensitive AFLP (MSAP). All species and populations exhibited moderate to high levels of genetic polymorphism irrespective of their ecological characteristics. Epigenetic diversity was greater than genetic diversity in all cases. Only in endemic species were the two variables positively related, but the difference between epigenetic and genetic diversity was greater at populations with low genetic polymorphism. Results revealed that the relationship between genetic and epigenetic diversity can be more complex than envisaged by the simple hypothesis addressed in this study, and highlight the need of additional research on the actual role of epigenetic variation as a source of phenotypic diversity before a realistic understanding of the evolutionary relevance of epigenetic phenomena in plant adaptation can be achieved.

Patterns of Genetic Diversity in Highly Invasive Species: Cogongrass (Imperata cylindrica) Expansion in the Invaded Range of the Southern United States (US)

The spatial expansions of invasive organisms in the novel range are generally expected to follow an isolation-by-distance relationship (IBD) if the invasion is biologically driven; however, many invasions are facilitated anthropogenically. This research focused on the extant expansion patterns of cogongrass (Imperata cylindrica). Cogongrass is a widespread invasive species throughout the southern United States (US). Patterns of infestation vary among US states. Cogongrass is pyrogenic, and its invasion threatens softwood (Pinus spp.) plantations, a substantial economic market for this US region. Over 600 individuals were sampled from seven invaded US states, using amplified fragment length polymorphisms (AFLPs) to assess genetic diversity and population structure. We suspected that differences in historical management efforts among US states influenced differences in genetic diversity and structure. We detected two genetic lineages at the highest level of analysis. One genetic lineage was locally restricted, whereas the other was found throughout the study region. Admixed individuals were found in all US states and consistently co-occurred with the dominant lineage, suggesting that secondary contact and hybridization may have facilitated expansion. The widespread prevalence of only one of the two detected genetic lineages suggests a primary genetic lineage responsible for on-going population expansion in the US.

Adaptive fitness of Sapindus emarginatus Vahl populations towards future climatic regimes and the limiting factors of its distribution

Sapindus emarginatus Vahl (Sapindaceae) also known as ‘Indian Soap nut’ is significantly important for saponin content in its fruits. However, its current population in India is heavily fragmented due to a lack of sustainable harvesting practices. Moreover, changing climatic regimes may further limit its distribution and possibly compromise the survival of the species in nature. The aim of the present study was to: predict the future distribution range of S. emarginatus; identify the bioclimatic variables limiting this distribution and to evaluate its adaptive fitness and genomic resilience towards these variables. To determine future species distribution range and identify limiting bioclimatic variables, we applied two different ecological niche models (ENMs; BioClim and MaxEnt) on real occurrence data (n = 88 locations). The adaptive fitness of the species was evaluated by quantifying the genetic variability with AFLP markers and marker-environmental associations, using AFLP-associated Bayesian statistics. We found 77% overlap between the baseline (2030) and predicted (2100) species distribution ranges, which were primarily determined by maximum temperature (T_MAX) and mean annual precipitation (MAP). The T_MAX and MAP contributed 43.1% and 27.1%, respectively to ENM model prediction. Furthermore, AFLP loci significantly associated with bioclimatic variables, and T_MAX and MAP represent the lowest proportion (6.15%), confirming to the severe response of the species genome towards these variables. Nevertheless, the very low Linkage disequilibrium (LD) in these loci (4.54%) suggests that the current sensitivity to T_MAX and MAP is subject to change during recombination. Moreover, a combination of high heterozygosity (0.40–0.43) and high within-population variability (91.63 ± 0.31%) confirmed high adaptive fitness to maintain reproductive success. Therefore, the current populations of S. emarginatus have substantial genomic resilience towards future climate change, albeit significant conservation efforts (including mass multiplication) are warranted to avoid future deleterious impacts of inbreeding depression on the fragmented populations.

STRUCTURE is more robust than other clustering methods in simulated mixed-ploidy populations

Analysis of population genetic structure has become a standard approach in population genetics. In polyploid complexes, clustering analyses can elucidate the origin of polyploid populations and patterns of admixture between different cytotypes. However, combining diploid and polyploid data can theoretically lead to biased inference with (artefactual) clustering by ploidy. We used simulated mixed-ploidy (diploid-autotetraploid) data to systematically compare the performance of k-means clustering and the model-based clustering methods implemented in STRUCTURE, ADMIXTURE, FASTSTRUCTURE and INSTRUCT under different scenarios of differentiation and with different marker types. Under scenarios of strong population differentiation, the tested applications performed equally well. However, when population differentiation was weak, STRUCTURE was the only method that allowed unbiased inference with markers with limited genotypic information (co-dominant markers with unknown dosage or dominant markers). Still, since STRUCTURE was comparatively slow, the much faster but less powerful FASTSTRUCTURE provides a reasonable alternative for large datasets. Finally, although bias makes k-means clustering unsuitable for markers with incomplete genotype information, for large numbers of loci (>1000) with known dosage k-means clustering was superior to FASTSTRUCTURE in terms of power and speed. We conclude that STRUCTURE is the most robust method for the analysis of genetic structure in mixed-ploidy populations, although alternative methods should be considered under some specific conditions.

Discerning between Two Tuscany (Italy) Ancient Apple cultivars, 'Rotella' and 'Casciana', through Polyphenolic Fingerprint and Molecular Markers

Ancient apple cultivars usually have higher nutraceutical value than commercial ones, but in most cases their variability in pomological traits does not allow us to discriminate among them. Fruit of two Tuscany ancient apple cultivars, ‘Casciana’ and ‘Rotella’, picked from eight different orchards (four for each cultivar) were analyzed for their pomological traits, organoleptic qualities, polyphenolic profile and antiradical activity. The effectiveness of a polyphenol-based cluster analysis was compared to molecular markers (internal transcribed spacers, ITS1 and ITS2) to unequivocally discern the two apples. ‘Casciana’ and ‘Rotella’ fruit had a higher nutraceutical value than some commercial cultivars, in terms of phenolic abundance, profile and total antiradical activity. Although pedo-climatic conditions of different orchards influenced the phenolic profile of both apples, the polyphenolic discriminant analysis clearly separated the two cultivars, principally due to higher amounts of procyanidin B2, procyanidin B3 and p-coumaroylquinic acid in ‘Casciana’ than in ‘Rotella’ fruit. These three polyphenols can be used proficiently as biochemical markers for distinguishing the two apples when pomological traits cannot. Conversely, ITS1 and ITS2 polymorphism did not allow us to distinguish ‘Casciana’ from ‘Rotella’ fruit. Overall, the use of polyphenolic fingerprint might represent a valid tool to ensure the traceability of products with a high economic value.

Morphological, genetic and epigenetic aspects of homoploid hybridization between Salvia officinalis L. and Salvia fruticosa Mill

The inheritance of phenotypic, genetic and epigenetic traits in hybridization events is difficult to predict, as numerous evolutionary, ecological, and genetic factors can play a crucial role in the process of hybridization. In the middle Adriatic island of Vis, we investigated hybridization between Salvia officinalis and S. fruticosa at morphological, genetic and epigenetic levels. SSR results revealed that hybrid individuals were characterized by diploid set of chromosomes suggesting homoploid hybridization. A well-defined group that mostly comprised of F1 generation individuals was detected. For the majority of analysed morphological characteristics, hybrids were placed in-between parental taxa, while at the same time, values of different genetic parameters were mostly higher in hybrids than in parental species. The results revealed a high contrast in the levels of phenotypic variability and epigenetic excitation between parental taxa. Environmental niche modelling confirmed that in the studied location S. officinalis experiences optimal climatological conditions, while S. fruticosa struggles with unsuitable conditions. Very low levels of gene flow between the parental species were detected. In addition, contrasting levels of epigenetic excitation in the studied groups clearly demonstrated the importance of an epigenetic response to an altered environment and confirmed the trans-generational nature of the epigenetic changes.

Long-term survival and successful conservation? Low genetic diversity but no evidence for reduced reproductive success at the north-westernmost range edge of Poa badensis (Poaceae) in Central Europe

Many steppe species reach their (north)westernmost distribution limit in western Central Europe. This also applies to Poa badensis, a rare steppe plant of calcareous rock/sand vegetation. To explore potential differences in reproductive success and genetic composition of peripheral populations, we analysed the absolute (north)westernmost occurrences in Western Germany and populations at the western margin (Eastern Austria) and the centre (Central Hungary) of the Pannonicum, representing a part of the continuous range. Specifically, we discuss the genetic and reproductive constitution of the (north)westernmost exclave and draw conclusions on the species' biogeographical and conservation history in this region. Therefore, we used two independent molecular marker systems (AFLPs, cpDNA sequences) and a set of performance parameters. Overall, lowest regional genetic diversity was found in Western Germany, which is mainly a result of the specific history of two populations. However, this low genetic diversity was not accompanied by reduced reproductive success. The Eastern Austrian populations showed reduced genetic diversity and predominantly reduced performance, interpreted as a consequence of small population sizes. Central Hungarian populations showed the overall highest genetic diversity and comparatively high performance values. We observed high admixture and haplotype sharing between Austrian and Hungarian populations, indicating gene flow among these regions. In contrast, we interpreted the increased population differentiation within, and the clear distinctiveness of the German exclave as a long-term isolation of these (north)westernmost occurrences. Our results, overall, prove the good constitution of these populations and, together with their particular biogeographical history, highlight their conservation value.

Polyploidy in Fruit Tree Crops of the Genus Annona (Annonaceae)

Genome duplication or polyploidy is one of the main factors of speciation in plants. It is especially frequent in hybrids and very valuable in many crops. The genus Annona belongs to the Annonaceae, a family that includes several fruit tree crops, such as cherimoya (Annona cherimola), sugar apple (Annona squamosa), their hybrid atemoya (A. cherimola × A. squamosa) or pawpaw (Asimina triloba). In this work, genome content was evaluated in several Annona species, A. triloba and atemoya. Surprisingly, while the hybrid atemoya has been reported as diploid, flow cytometry analysis of a progeny obtained from an interspecific cross between A. cherimola and A. squamosa showed an unusual ploidy variability that was also confirmed karyotype analysis. While the progeny from intraspecific crosses of A. cherimola showed polyploid genotypes that ranged from 2.5 to 33%, the hybrid atemoyas from the interspecific cross showed 35% of triploids from a total of 186 genotypes analyzed. With the aim of understanding the possible implications of the production of non-reduced gametes, pollen performance, pollen size and frequency distribution of pollen grains was quantified in the progeny of this cross and the parents. A large polymorphism in pollen grain size was found within the interspecific progeny with higher production of unreduced pollen in triploids (38%) than in diploids (29%). Moreover, using PCR amplification of selected microsatellite loci, while 13.7% of the pollen grains from the diploids showed two alleles, 41.28% of the grains from the triploids amplified two alleles and 5.63% showed up to three alleles. This suggests that the larger pollen grains could correspond to diploid and, in a lower frequency, to triploid pollen. Pollen performance was also affected with lower pollen germination in the hybrid triploids than in both diploid parents. The results confirm a higher percentage of polyploids in the interspecific cross, affecting pollen grain size and pollen performance. The occurrence of unreduced gametes in A. cherimola, A. squamosa and their interspecific progeny that may result in abnormalities of ploidy such as the triploids and tetraploids observed in this study, opens an interesting opportunity to study polyploidy in Annonaceae.

The Promise of Molecular and Genomic Techniques for Biodiversity Research and DNA Barcoding of the Arabian Peninsula Flora

The Arabian Peninsula is known to have a comprehensive and rich endowment of unique and genetically diverse plant genetic resources. Analysis and conservation of biological diversity is a crucial issue to the whole Arabian Peninsula. The rapid and accurate delimitation and identification of a species is crucial to genetic diversity analysis and the first critical step in the assessment of distribution, population abundance and threats related to a particular target species. During the last two decades, classical strategies of evaluating genetic variability, such as morphology and physiology, have been greatly complemented by phylogenetic, taxonomic, genetic diversity and breeding research molecular studies. At present, initiatives are taking place around the world to generate DNA barcode libraries for vascular plant flora and to make these data available in order to better understand, conserve and utilize biodiversity. The number of herbarium collection-based plant evolutionary genetics and genomics studies being conducted has been increasing worldwide. The herbaria provide a rich resource of already preserved and identified material, and these as well as freshly collected samples from the wild can be used for creating a reference DNA barcode library for the vascular plant flora of a region. This review discusses the main molecular and genomic techniques used in plant identification and biodiversity analysis. Hence, we highlight studies emphasizing various molecular techniques undertaken during the last 10 years to study the plant biodiversity of the Arabian Peninsula. Special emphasis on the role of DNA barcoding as a powerful tool for plant biodiversity analysis is provided, along with the crucial role of herbaria in creating a DNA barcode library.

Systems biology approaches in the study of Chinese herbal formulae

Systems biology is an academic field that attempts to integrate different levels of information to understand how biological systems function. It is the study of the composition of all components of a biological system and their interactions under specific conditions. The core of systems biology is holistic and systematic research, which is different from the manner of thinking and research of all other branches of biology to date. Chinese herbal formulae (CHF) are the main form of Chinese medicine and are composed of single Chinese herbal medicines (CHMs) with pharmacological and pharmacodynamic compatibility. When single CHMs are combined into CHF, the result is different from the original effect of a single drug and can be better adapted to more diseases with complex symptoms. CHF represent a complex system with multiple components, targets and effects. Therefore, the use of systems biology is conducive to revealing the complex characteristics of CHF. With the rapid development of omics technologies, systems biology has been widely and increasingly applied to the study of the basis of the pharmacological substances, action targets and mechanisms of CHF. To meet the challenges of multiomics synthesis-intensive studies and system dynamics research in CHF, this paper reviews the common techniques of genomics, transcriptomics, proteomics, metabolomics, and metagenomics and their applications in research on CHF.

Differences in the fungal communities nursed by two genetic groups of the alpine cushion plant, Silene acaulis

Foundation plants shape the composition of local biotic communities and abiotic environments, but the impact of a plant's intraspecific variations on these processes is poorly understood. We examined these links in the alpine cushion moss campion (Silene acaulis) on two neighboring mountain ranges in the French Alps. Genotyping of cushion plants revealed two genetic clusters matching known subspecies. The exscapa subspecies was found on both limestone and granite, while the longiscapa one was only found on limestone. Even on similar limestone bedrock, cushion soils from the two S. acaulis subspecies deeply differed in their impact on soil abiotic conditions. They further strikingly differed from each other and from the surrounding bare soils in fungal community composition. Plant genotype variations accounted for a large part of the fungal composition variability in cushion soils, even when considering geography or soil chemistry, and particularly for the dominant molecular operational taxonomic units (MOTUs). Both saprophytic and biotrophic fungal taxa were related to the MOTUs recurrently associated with a single plant genetic cluster. Moreover, the putative phytopathogens were abundant, and within the same genus (Cladosporium) or species (Pyrenopeziza brassicae), MOTUs showing specificity for each plant subspecies were found. Our study highlights the combined influences of bedrock and plant genotype on fungal recruitment into cushion soils and suggests the coexistence of two mechanisms, an indirect selection resulting from the colonization of an engineered soil by free-living saprobes and a direct selection resulting from direct plant-fungi interactions.

Dual pathways in social evolution: Population genetic structure of group-living and solitary species of kleptoparasitic spiders (Argyrodinae: Theridiidae)

Group-living behavior is taxonomically widespread but rare in spiders. The conventional view is that the main pathways to group-living in spiders are either sub-social, where extended maternal care leads to prolonged sibling association; or communal living, where individuals aggregate to exploit a common resource. Female egg-sac guarding behavior occurs throughout kleptoparasitic spiders in the subfamily Argyrodinae (Theridiidae), while individuals in group-living species cohabit in the resource rich webs of their host spiders. These attributes fit both sub-social and communal routes to group-living, which offers new insights to study the early stages of social evolution. We investigated whether members of kleptoparasitic groups in natural populations comprise related individuals by comparing the population structure of two group-living species, Argyrodes miniaceus and A. cf. fissifrons, and two solitary species, A. fasciatus and Neospintharus trigonum. We found that: (1) genetic-spatial autocorrelation in group-living species was highest among spiders sharing the same host web and declined steeply with increasing distance, but no significant autocorrelation at any scale for solitary species; (2) there was high relatedness among group members in two cases of group-living species, which indicated relatedness was not an adhesive agent in most of the groups, but no high relatedness in solitary species; and (3) the host web boundary was not the sole predictor of genetic structures in group-living species. These results suggest that population genetic structure in the group-living species is caused by limited dispersal of group members that is favored by ecological conditions, including the nature and size of resources. In contrast, the absence of genetic structuring in populations of solitary species indicates a high level of dispersal with individual interactions unlikely to have fitness benefits.

Conservation genetics of two threatened frogs from the Mambilla highlands, Nigeria

Amphibians are the vertebrate group with the highest number of species threatened with extinction, and habitat loss and fragmentation are considered to be among the leading causes of their declines and extinctions. Little is known of the population biology of amphibian species inhabiting montane forests in Central and West Africa, where anthropogenic activities such as farming and cattle raising are major threats to native biodiversity. We used Amplified Fragment Length Polymorphisms (AFLPs) to assess the population genetic structure of two poorly known species, Cardioglossa schioetzi and Leptodactylodon bicolor (both in the Arthroleptidae), in and around Ngel Nyaki Forest Reserve on the Mambilla Plateau in eastern Nigeria. The landscape comprises continuous forest on steep slopes and small riparian forest fragments in a grassland matrix. While increased fragmentation is well documented for these and other forests in the mountains of Cameroon and Nigeria over the past century, there are no previous assessments of the impact of forest fragmentation on montane amphibian populations in this region. Our estimates of genetic diversity are similar across populations within each species with levels of heterozygosity values consistent with local population declines. Except for a pair of populations (C. schioetzi) we did not observe genetic differentiation between forest and riparian forest fragment populations, nor across sites within continuous forest (L. bicolor). Our results demonstrate recent gene flow between forest fragments and the adjacent protected forests and suggest that small forest corridors connecting these may lessen the genetic consequences of at least 30 years of intense and severe fragmentation in Ngel Nyaki.

Analysis of genetic polymorphisms and tropism in East African Leishmania donovani by Amplified Fragment Length Polymorphism and kDNA minicircle sequencing

Visceral leishmaniasis (VL), the most severe form of leishmaniasis, is caused by Leishmania donovani. In addition to fatal VL, these parasites also cause skin diseases in immune-competent and -suppressed people, post-kala azar dermal leishmaniasis (PKDL) and HIV/VL co-infections, respectively. Genetic polymorphism in 36 Ethiopian and Sudanese L. donovani strains from VL, PKDL and HIV/VL patients was examined using Amplified Fragment Length Polymorphism (AFLP), kDNA minicircle sequencing and Southern blotting. Strains were isolated from different patient tissues: in VL from lymph node, spleen or bone marrow; and in HIV/VL from skin, spleen or bone marrow. When VL and PKDL strains from the same region in Sudan were examined by Southern blotting using a DNA probe to the L. donovani 28S rRNA gene only minor differences were observed. kDNA sequence analysis distributed the strains in no particular order among four clusters (A - D), while AFLP analysis grouped the strains according to geographical origin into two major clades, Southern Ethiopia (SE) and Sudan/Northern Ethiopia (SD/NE). Strains in the latter clade were further divided into subpopulations by zymodeme, geography and year of isolation, but not by clinical symptoms. However, skin isolates showed significantly (p < 0.0001) fewer polymorphic AFLP fragments (average 10 strains = 348.6 ± 8.1) than VL strains (average 26 strains = 383.5 ± 3.8).

Mould spoilage of foods and beverages: Using the right methodology

Fungal spoilage of products manufactured by the food and beverage industry imposes significant annual global revenue losses. Mould spoilage can also be a food safety issue due to the production of mycotoxins by these moulds. To prevent mould spoilage, it is essential that the associated mycobiota be adequately isolated and accurately identified. The main fungal groups associated with spoilage are the xerophilic, heat-resistant, preservative-resistant, anaerobic and psychrophilic fungi. To assess mould spoilage, the appropriate methodology and media must be used. While classic mycological detection methods can detect a broad range of fungi using well validated protocols, they are time consuming and results can take days or even weeks. New molecular detection methods are faster but require good DNA isolation techniques, expensive equipment and may detect viable and non-viable fungi that probably will not spoil a specific product. Although there is no complete and easy method for the detection of fungi in food it is important to be aware of the limitation of the methodology. More research is needed on the development of methods of detection and identification that are both faster and highly sensitive.

Hierarchical structure of ecological and non-ecological processes of differentiation shaped ongoing gastropod radiation in the Malawi Basin

Ecological processes, non-ecological processes or a combination of both may cause reproductive isolation and speciation, but their specific roles and potentially complex interactions in evolutionary radiations remain poorly understood, which defines a central knowledge gap at the interface of microevolution and macroevolution. Here I examine genome scans in combination with phenotypic and environmental data to disentangle how ecological and non-ecological processes contributed to population differentiation and speciation in an ongoing radiation of Lanistes gastropods from the Malawi Basin. I found a remarkable hierarchical structure of differentiation mechanisms in space and time: neutral and mutation-order processes are older and occur mainly between regions, whereas more recent adaptive processes are the main driver of genetic differentiation and reproductive isolation within regions. The strongest differentiation occurs between habitats and between regions, i.e. when ecological and non-ecological processes act synergistically. The structured occurrence of these processes based on the specific geographical setting and ecological opportunities strongly influenced the potential for evolutionary radiation. The results highlight the importance of interactions between various mechanisms of differentiation in evolutionary radiations, and suggest that non-ecological processes are important in adaptive radiations, including those of cichlids. Insight into such interactions is critical to understanding large-scale patterns of organismal diversity.

Early-Mid Pleistocene genetic differentiation and range expansions as exemplified by invasive Eurasian Bunias orientalis (Brassicaceae) indicates the Caucasus as key region

Turkish Warty cabbage, Bunias orientalis L. (Brassicaceae) is a perennial herb known for its 250 years of invasion history into Europe and worldwide temperate regions. Putative centers of origin were debated to be located in Turkey, the Caucasus or Eastern Europe. Based on the genetic variation from the nuclear and plastid genomes, we identified two major gene pools in the Caucasian-Irano-Turanian region and close to the Northern Caucasus, respectively. These gene pools are old and started to diverge and expand approximately 930 kya in the Caucasus. Pleistocene glaciation and deglaciation cycles favoured later expansion of a European gene pool 230 kya, which was effectively separated from the Caucasian-Irano-Turanian gene pool. Although the European gene pool is genetically less diverse, it has largely served as source for colonization of Western and Northern Europe in modern times with rare observations of genetic contributions from the Caucasian-Irano-Turanian gene pool such as in North-East America. This study largely utilized herbarium material to take advantage of a biodiversity treasure trove providing biological material and also giving access to detailed collection information.

Use of AFLP for the study of eukaryotic pathogens affecting humans

Amplified fragment length polymorphism (AFLP) is a genotyping technique based on PCR amplification of specific restriction fragments from a particular genome. The methodology has been extensively used in plant biology to solve a variety of scientific questions, including taxonomy, molecular epidemiology, systematics, population genetics, among many others. The AFLP share advantages and disadvantages with other types of molecular markers, being particularly useful in organisms with no previous DNA sequence knowledge. In eukaryotic pathogens, the technique has not been extensively used, although it has the potential to solve many important issues as it allows the simultaneous examination of hundreds or even thousands of polymorphic sites in the genome of the organism. Here we describe the main applications published on the use of AFLP in eukaryotic pathogens, with emphasis in species of the groups fungi, protozoa and helminths, and discuss the role of this methodology in the context of new techniques derived from the advances of the next generation sequencing.

Dealing with AFLP genotyping errors to reveal genetic structure in Plukenetia volubilis (Euphorbiaceae) in the Peruvian Amazon

An analysis of the population structure and genetic diversity for any organism often depends on one or more molecular marker techniques. Nonetheless, these techniques are not absolutely reliable because of various sources of errors arising during the genotyping process. Thus, a complex analysis of genotyping error was carried out with the AFLP method in 169 samples of the oil seed plant Plukenetia volubilis L. from small isolated subpopulations in the Peruvian Amazon. Samples were collected in nine localities from the region of San Martin. Analysis was done in eight datasets with a genotyping error from 0 to 5%. Using eleven primer combinations, 102 to 275 markers were obtained according to the dataset. It was found that it is only possible to obtain the most reliable and robust results through a multiple-level filtering process. Genotyping error and software set up influence both the estimation of population structure and genetic diversity, where in our case population number (K) varied between 2–9 depending on the dataset and statistical method used. Surprisingly, discrepancies in K number were caused more by statistical approaches than by genotyping errors themselves. However, for estimation of genetic diversity, the degree of genotyping error was critical because descriptive parameters (He, F_ST, PLP 5%) varied substantially (by at least 25%). Due to low gene flow, P. volubilis mostly consists of small isolated subpopulations (Φ_PT = 0.252–0.323) with some degree of admixture given by socio-economic connectivity among the sites; a direct link between the genetic and geographic distances was not confirmed. The study illustrates the successful application of AFLP to infer genetic structure in non-model plants.

No obvious genetic erosion, but evident relict status at the westernmost range edge of the Pontic-Pannonian steppe plant Linum flavum L. (Linaceae) in Central Europe

We investigate patterns of genetic variation along an east–west transect of Central European populations of Linum flavum and interpret the Quaternary history of its peripheral populations, especially those at the westernmost isolated range edge, discussing their migrations and possible relict status. We defined our peripheral transect across three study regions from Central Hungary, eastern Austria to southwestern Germany. Using AFLP fingerprinting and cpDNA sequence variation (rpL16 intron, atpI‐H), we analyzed 267 and 95 individuals, respectively, representing each study region by four populations. Hierarchical AMOVA (AFLPs) indicated significant variation among study regions (12% of total variance) and moderate differentiation between populations (10%). Population differentiation was high at the westernmost range edge (11.5%, Germany), but also in the east (13.4%, Hungary), compared to the Austrian study region (8.6%). Correspondingly, AFLP diversity was highest in the center of the study transect in eastern Austria. CpDNA haplotypes support a pattern of regional structuring with the strongest separation of the westernmost range edge, and some haplotype sharing among Austrian and Hungarian individuals. Equilibrating nucleotide versus haplotype diversity patterns, the highly diverse populations at the Pannonian range edge (Austria) indicate long‐term persistence, while Central Pannonian populations are obviously effected by recent bottlenecks. Intermediate nucleotide, but high haplotype diversity within the westernmost exclave (Swabian Alb), is indicative of a founder bottleneck during its pre‐LGM or early postglacial migration history, followed by sufficient time to accumulate cpDNA variation. The not obviously reduced genetic diversity and distinctiveness of L. flavum at the westernmost range edge suggest a long‐term persistence (relict status) of populations in this region, where the species has survived probably even the Würm glaciation in extra‐Mediterranean refugia. This genetic relict variation represents an important part of the overall genetic diversity found in the western periphery of this steppe plant and highlights the high conservation priority of respective gene pools.

Do genome size differences within Brachionus asplanchnoidis (Rotifera, Monogononta) cause reproductive barriers among geographic populations?

Genome size in the rotifer Brachionus asplanchnoidis, which belongs to the B. plicatilis species complex, is greatly enlarged and extremely variable (205-407 Mbp). Such variation raises the question whether large genome size differences among individuals might cause reproductive barriers, which could trigger speciation within this group by restricting gene flow across populations. To test this hypothesis, we used B. asplanchnoidis clones from three geographic populations and conducted assays to quantify reproductive isolation among clones differing in genome size, and we examined the population structure of all three populations using amplified fragment length polymorphisms (AFLPs). AFLPs indicated that these populations were genetically separated, but we also found hints of natural gene flow. Clones from different populations with genome size differences of up to 1.7-fold could interbred successfully in the laboratory and give rise to viable, fertile 'hybrid' offspring. Genome sizes of these 'hybrids' were intermediate between those of their parents, and fitness in terms of male production, population growth, and egg development time was not negatively affected. Thus, we found no evidence for reproductive isolation or nascent speciation within B. asplanchnoidis. Instead, our results suggest that gene flow within this species can occur despite a remarkably large range of genome sizes.

Discrimination of Picea chihuahuana Martinez populations on the basis of climatic, edaphic, dendrometric, genetic and population traits

Background

Picea chihuahuana, which is endemic to Mexico, is currently listed as “Endangered” on the Red List. Chihuahua spruce is only found in the Sierra Madre Occidental (SMO), Mexico. About 42,600 individuals are distributed in forty populations. These populations are fragmented and can be classified into three geographically distinct clusters in the SMO. The total area covered by P. chihuahuana populations is less than 300 ha. A recent study suggested assisted migration as an alternative to the ex situ conservation of P. chihuahuana, taking into consideration the genetic structure and diversity of the populations and the predictions regarding the future climate of the habitat. However, detailed background information is required to enable development of plans for protecting and conserving species and for successful assisted migration. Thus, it is important to identify differences between populations in relation to environmental conditions. The genetic diversity of populations, which affect vigor, evolution and adaptability of the species, must also be considered. In this study, we examined 14 populations of P. chihuahuana, with the overall aim of discriminating the populations and form clusters of this species.

Methods

Each population was represented by one 50 × 50 m plot established in the center of its respective location. Climate, soil, dasometric, density variables and genetic and species diversities were assessed in these plots for further analyses. The putatively neutral and adaptive AFLP markers were used to calculate genetic diversity. Affinity Propagation (AP) clustering technique and k-means clustering algorithm were used to classify the populations in the optimal number of clusters. Later stepwise binomial logistic regression was applied to test for significant differences in variables of the southern and northern P. chihuahuana populations. Spearman’s correlation test was used to analyze the relationships among all variables studied.

Results

The binomial logistic regression analysis revealed that seven climate variables, the geographical longitude and sand proportion in the soil separated the southern from northern populations. The northern populations grow in more arid and continental conditions and on soils with lower sand proportion. The mean genetic diversity using all AFLP studied of P. chihuahuana was significantly correlated with the mean temperature in the warmest month, where warmer temperatures are associated to larger genetic diversity. Genetic diversity of P. chihuahuana calculated with putatively adaptive AFLP was not statistically significantly correlated with any environmental factor.

Discussion

Future reforestation programs should take into account that at least two different groups (the northern and southern cluster) of P. chihuahuana exist, as local adaptation takes place because of different environmental conditions.

Geographic barriers and Pleistocene climate change shaped patterns of genetic variation in the Eastern Afromontane biodiversity hotspot

The Eastern African Afromontane forest is getting increased attention in conservation studies because of its high endemicity levels and shrinking geographic distribution. Phylogeographic studies have found evidence of high levels of genetic variation structured across the Great Rift System. Here, we use the epiphytic plant species Canarina eminii to explore causal explanations for this pattern. Phylogeographic analyses were undertaken using plastid regions and AFLP fragments. Population genetic analyses, Statistical Parsimony, and Bayesian methods were used to infer genetic diversity, genealogical relationships, structure, gene flow barriers, and the spatiotemporal evolution of populations. A strong phylogeographic structure was found, with two reciprocally monophyletic lineages on each side of the Great Rift System, high genetic exclusivity, and restricted gene flow among mountain ranges. We explain this pattern by topographic and ecological changes driven by geological rifting in Eastern Africa. Subsequent genetic structure is attributed to Pleistocene climatic changes, in which sky-islands acted as long-term refuges and cradles of genetic diversity. Our study highlights the importance of climate change and geographic barriers associated with the African Rift System in shaping population genetic patterns, as well as the need to preserve the high levels of exclusive and critically endangered biodiversity harboured by current patches of the Afromontane forest.

Boxer crabs induce asexual reproduction of their associated sea anemones by splitting and intraspecific theft

Crabs of the genus Lybia have the remarkable habit of holding a sea anemone in each of their claws. This partnership appears to be obligate, at least on the part of the crab. The present study focuses on Lybia leptochelis from the Red Sea holding anemones of the genus Alicia (family Aliciidae). These anemones have not been found free living, only in association with L. leptochelis. In an attempt to understand how the crabs acquire them, we conducted a series of behavioral experiments and molecular analyses. Laboratory observations showed that the removal of one anemone from a crab induces a “splitting” behavior, whereby the crab tears the remaining anemone into two similar parts, resulting in a complete anemone in each claw after regeneration. Furthermore, when two crabs, one holding anemones and one lacking them, are confronted, the crabs fight, almost always leading to the “theft” of a complete anemone or anemone fragment by the crab without them. Following this, crabs “split” their lone anemone into two. Individuals of Alicia sp. removed from freshly collected L. leptochelis were used for DNA analysis. By employing AFLP (Fluorescence Amplified Fragments Length Polymorphism) it was shown that each pair of anemones from a given crab is genetically identical. Furthermore, there is genetic identity between most pairs of anemone held by different crabs, with the others showing slight genetic differences. This is a unique case in which one animal induces asexual reproduction of another, consequently also affecting its genetic diversity.

Geography shapes the phylogeny of frailejones (Espeletiinae Cuatrec., Asteraceae): a remarkable example of recent rapid radiation in sky islands

Background

The páramo ecosystem, located above the timberline in the tropical Andes, has been the setting for some of the most dramatic plant radiations, and it is one of the world’s fastest evolving and most diverse high-altitude ecosystems. Today 144+ species of frailejones (subtribe Espeletiinae Cuatrec., Asteraceae) dominate the páramo. Frailejones have intrigued naturalists and botanists, not just for their appealing beauty and impressive morphological diversity, but also for their remarkable adaptations to the extremely harsh environmental conditions of the páramo. Previous attempts to reconstruct the evolutionary history of this group failed to resolve relationships among genera and species, and there is no agreement regarding the classification of the group. Thus, our goal was to reconstruct the phylogeny of the frailejones and to test the influence of the geography on it as a first step to understanding the patterns of radiation of these plants.

Methods

Field expeditions in 70 páramos of Colombia and Venezuela resulted in 555 collected samples from 110 species. Additional material was obtained from herbarium specimens. Sequence data included nrDNA (ITS and ETS) and cpDNA (rpl16), for an aligned total of 2,954 bp. Fragment analysis was performed with AFLP data using 28 primer combinations and yielding 1,665 fragments. Phylogenies based on sequence data were reconstructed under maximum parsimony, maximum likelihood and Bayesian inference. The AFLP dataset employed minimum evolution analyses. A Monte Carlo permutation test was used to infer the influence of the geography on the phylogeny.

Results

Phylogenies reconstructed suggest that most genera are paraphyletic, but the phylogenetic signal may be misled by hybridization and incomplete lineage sorting. A tree with all the available molecular data shows two large clades: one of primarily Venezuelan species that includes a few neighboring Colombian species; and a second clade of only Colombian species. Results from the Monte Carlo permutation test suggests a very strong influence of the geography on the phylogenetic relationships. Venezuelan páramos tend to hold taxa that are more distantly-related to each other than Colombian páramos, where taxa are more closely-related to each other.

Conclusions

Our data suggest the presence of two independent radiations: one in Venezuela and the other in Colombia. In addition, the current generic classification will need to be deeply revised. Analyses show a strong geographic structure in the phylogeny, with large clades grouped in hotspots of diversity at a regional scale, and in páramo localities at a local scale. Differences in the degrees of relatedness between sympatric species of Venezuelan and Colombian páramos may be explained because of the younger age of the latter páramos, and the lesser time for speciation of Espeletiinae in them.