Median-joining Network Analysis Research Articles

Evolution of maize landraces in southwest China: Evidence from the globulin1 gene

To explore the evolution of maize landraces from southwest China, we conducted a population genetic analysis of DNA sequence variation in globulin1 (Glb1) gene from 71 individuals representing the maize landrace, common maize, parviglumis, Zea luxurians, and Tripsacum dactyloides. We tested 477 variable, 800 conserved, and 253 informative sites in the Glb1 gene sequences. On the basis of πˆ per base pair and θˆ per base pair, the highest level of sequence variation was detected in parviglumis, followed by maize landraces and common maize. Z. luxurians and T. dactyloides retained a low level of variation. For Glb1 gene, negative or almost zero estimates for Tajima's D and Fu and Li's statistics in the 8 taxa, show that neutral evolution can be accepted. A large number of shared polymorphisms existed with no fixed differences between parviglumis and both the maize landrace and common maize. Maximum Likelihood (ML) analysis showed that sequences from maize landraces, common maize, parviglumis, and Z. luxurians were separated into two well-supported clades, and sequences from T. dactyloides constituted a distinct group. Excluding T. dactyloides and Z. luxurians, median-joining (MJ) network analysis clustered the remaining taxa into five haplotypes, revealing a higher level of haplotype diversity in the landrace. The findings suggest that the maize landrace in southwest China was domesticated from parviglumis and first introduced to Sichuan from India via Tibet.

East African pigs have a complex Indian, Far Eastern and Western ancestry.

In this study, we have characterized the mitochondrial diversity of 81 swine from Uganda. Median-joining network analysis of D-loop sequences from these individuals and others characterized in previous studies allowed us to determine that Ugandan pigs cluster with populations from the West (Europe/North Africa), Far East and India. In addition, partial sequencing of the Y-chromosome UTY locus in 18 Ugandan domestic pigs revealed the segregation of a single HY1 lineage that has a cosmopolitan distribution. A Western and Far Eastern ancestry for East African pigs had been already reported, but this is the first study demonstrating an additional contribution from the Indian porcine gene pool. This result is consistent with the high frequency of zebuine alleles in cattle from East Africa. The geographic coordinates of East Africa, at the crossroads of many trading routes that, through the ages, linked Europe, Africa and Asia, might explain the rich and complex genetic heritage of livestock native to this area.

Population genetics and demographic history of guava fruit fly Bactrocera correcta (Diptera: Tephritidae) in northeastern Thailand

Bactrocera correcta (Bezzi) is among the most destructive fruit fly pests of the genus Bactrocera. This species infests 62 species of plants belonging 30 families, many of which are commercially important. In this study, the genetic structure, diversity and demographic history of B. correcta in Thailand were inferred from mitochondrial cytochrome c oxidase I (COI) sequences. High genetic diversity was recorded in the 171 samples collected from 15 locations. This was due largely to the existence of two divergent lineages (I, II) revealed by median joining (MJ) network analysis. Genetic structure analysis revealed an overall low level of genetic differentiation between populations suggesting that the flies can move freely across geographic regions. Because the host plants are commonly grown in Thailand, continuity of habitats is the factor most likely responsible for the genetic homogeneity. In addition, the recent population history could also be a factor that contributed to the overall low level of the genetic structure. Mismatch distribution analysis as well as Tajima's D and Fu's FS tests detected evidence of recent demographic expansion dating back to the end of the last glaciations.

Genetic analysis of river, swamp and hybrid buffaloes of north‐east India throw new light on phylogeography of water buffalo (Bubalus bubalis)

This study analysed buffaloes from north-east India and compared their nuclear and mitochondrial DNA variations with buffaloes of mainland India, China, Mediterranean and South-East Asia. Microsatellite genotypes of 338 buffaloes including 210 from six north-east Indian buffalo populations and three mainland Indian breeds were analysed to evaluate their genetic structure and evolutionary relationships. Phylogenetic analysis and multidimensional scaling plot of pairwise FST revealed the clustering of all swamp-type buffaloes of north-east India with Lower Assamese (significantly hybrid type) buffaloes in one plane and all the mainland river buffaloes in another plane while the upper Assamese buffaloes being distinct from both these clusters. Analysis of mtDNA D-loop region of 530-bp length was performed on 345 sequences belonging to 23 buffalo populations from various geographical regions to establish the phylogeography of Indian water buffalo. The swamp buffaloes of north-east India clustered with both the lineages of Chinese swamp buffalo. Multidimensional scaling display of pairwise FST derived from mitochondrial DNA data showed clustering of upper Assamese, Chilika and Mediterranean buffaloes distinctly from all the other Indian buffalo populations. Median-joining network analysis further confirmed the distinctness and ancestral nature of these buffaloes. The study revealed north-east region of India forming part of the wider hybrid zone of water buffalo that may probably extend from north-east India to South-East Asia.

Holocene southward expansion in seasonally dry tropical forests in South America: phylogeography ofFicus bonijesulapensis(Moraceae)

We conducted a phylogeographical and niche modelling study of the tree Ficus bonijesulapensis, endemic to Brazilian seasonally dry tropical forests (SDTFs), in order to evaluate the effects of Quaternary climatic fluctuations on population dynamics. The trnQ–5′rps16 region of plastid DNA was sequenced from 15 populations. Three phylogeographical groups were identified by the median-joining algorithm network and spatial analysis of molecular variance (SAMOVA) (FCT = 0.591): a central-west, a central-east and a scattered group. The central groups had higher total haplotype and nucleotide diversities than the scattered group. Ecological niche modelling suggested that, since the Last Interglacial (130 kyr bp), the central and north regions have been relatively stable, whereas the southern region of the species distribution has been less stable. The phylogeographical groups showed concordance with the floristic units described for SDTFs. The low genetic diversity, unimodal mismatch distribution and unfavourable climatic conditions in the southern region suggest a recent southward expansion of the range of the species during the Holocene, supporting the hypothesis of the southward expansion of SDTFs during this period. The central and northern regions of the current distribution of F. bonijesulapensis, which are consistent with arboreal caatinga and rock outcrop floristic units, were potential refugia during Quaternary climatic fluctuations.

Interleukin-37 gene variants segregated anciently coexist during hominid evolution.

IL37 is a member of IL-1 cytokine family but conveys anti-inflammatory functions. The biological characteristic and genetic heterogeneity of IL37 are not fully understood yet. Here using the whole-genome sequencing data from 1000 Genomes Project, we performed population and evolutionary genetic analysis of human IL37 gene. First, 2184 IL37 gene sequences from different human populations were retrieved. The IL37 protein sequences were inferred from the coding DNA sequences and multiple species alignment was made. Then, the phylogenetic tree of IL37 was built and dN/dS ratios were calculated for each evolutionary branch, the classic McDonald and Kreitman test was also performed. Next, we conducted intraspecific evolutionary genetic analysis and built the genealogy network of 116 unique IL37 haplotypes through median-joining network analysis. Finally, we compared IL37 sequences between the modern and archaic humans. Our results for the first time provide solid evidence that common IL37 variants other than NCBI reference sequence are present worldwide. Our data also supports that IL37 variants are shaped and maintained by selection instead of neutral evolution. We further identified that human IL37 variants consist of two major haplogroups and their presence in archaic humans corroborates its ancient origin in hominid evolution. In conclusion, these data indicate that common IL37 variants are maintained among human populations by selective force, suggesting their potential involvements in immune regulation and human diseases. In addition, the ancient history of IL37 variants reveals interesting insight into the complicated human evolutionary history.

Genetic structure of Scomber japonicus (Perciformes: Scombridae) along the coast of China revealed by complete mitochondrial cytochrome b sequences

The phylogeography history and contemporary agents of selection for many marine fisheries, characterized by widespread species distributions in the face of significant harvest, remains poorly understood. Chub mackerel (Scomber japonicus) are a widespread species in the Indo-Pacific and represent one of the top five commercially fished species in the world, yet their phylogeographic history remains unknown. We characterized the genetic diversity, structure and demographic history of S. japonicus throughout adjacent Chinese seas (from the Yellow Sea to the South China Sea). Using 220 individuals from 11 sites, we inferred 55 distinct haplotypes from complete mitochondrial cytochrome b gene sequences. Haplotype diversity ranged from 0.505 to 0.967 and nucleotide diversity ranged from 0.00056 to 0.01042. Genetic differentiation (Fst) statistics suggested that the highest level of differentiation existed between the SanYa and SanSha localities (Fst = 0.86977), while the lowest levels of differentiation occurred between the DongGang and ShiDao localities (Fst ∼ 0). Kimura’s genetic distances ranged from 0.001 to 0.011 within and from 0.001 to 0.018 between populations. Hierarchical analysis of molecular variance, Neighbor-joining and median-joining network analyses identified significant phylogeographic structure with two localities (SanYa, Hainan of the South China Sea and LianYunGang, Jiangsu of the East China Sea) explaining most of the genetic variation observed, while the remaining populations were poorly differentiated.

Molecular phylogenetic identification of Fasciola flukes in Nepal

Eighty-one Fasciola flukes collected from 8 districts in Nepal were analyzed for their species identification on the basis of their spermatogenic status and nuclear ribosomal internal transcribed spacer 1 (ITS1) and for their phylogenetic relation with Fasciola flukes from other Asian countries on the basis of the mitochondrial NADH dehydrogenase subunit 1 (nad1) gene. Sixty-one flukes (75.3%) were aspermic Fasciola sp., and 20 flukes (24.7%) were identified as Fasciola gigantica. All of the aspermic flukes displayed the Fh/Fg type in ITS1, which was predominant in aspermic Fasciola sp. from China, and most (60 flukes) displayed the Fsp-ND1-N1 haplotype in the nad1, which had an identical nucleotide sequence to the major haplotype (Fg-C2) of the aspermic flukes from China. These results suggest that aspermic Fasciola sp. was introduced into Nepal from China. Furthermore, the results of the diversity indices, neutrality indices, and median-joining network analysis with reference haplotypes from Asian countries suggest that aspermic Fasciola sp. rapidly expanded its distribution. In contrasts, F. gigantica displayed 10 nad1 haplotypes, which showed higher population diversity indices than the haplotypes of aspermic flukes, indicating that the F. gigantica population was clearly distributed in Nepal earlier than the aspermic Fasciola population. Although the F. gigantica haplotypes from Nepal formed a star-like phylogeny consisting of a main founder haplotype (Fg-ND1-N1), together with some F. gigantica haplotypes from Myanmar and Thailand, the Nepal population differed genetically from F. gigantica populations of neighboring countries as each country had distinct founder haplotype(s).

Genetic variation of the greenhouse whitefly,Trialeurodes vaporariorum(Hemiptera: Aleyrodidae), among populations from Serbia and neighbouring countries, as inferred fromCOIsequence variability

The greenhouse whitefly Trialeurodes vaporariorum Westwood, 1856 (Hemiptera: Aleyrodidae) is an invasive and highly polyphagous phloem-feeding pest of vegetables and ornamentals. Trialeurodes vaporariorum causes serious damage due to direct feeding and transmits several important plant viruses. Excessive use of insecticides has resulted in significantly reduced levels of susceptibility of various T. vaporariorum populations. To determine the genetic variability within and among populations of T. vaporariorum from Serbia and to explore their genetic relatedness with other T. vaporariorum populations, we analysed the mitochondrial cytochrome c oxidase I (COI) sequences of 16 populations from Serbia and six neighbouring countries: Montenegro (three populations), Macedonia (one population) and Croatia (two populations), for a total of 198 analysed specimens. A low overall level of sequence divergence and only five variable nucleotides and six haplotypes were found. The most frequent haplotype, H1, was identified in all Serbian populations and in all specimens from distant localities in Croatia and Macedonia. The COI sequence data that was retrieved from GenBank and the data from our study indicated that H1 is the most globally widespread T. vaporariorum haplotype. A lack of spatial genetic structure among the studied T. vaporariorum populations, as well as two demographic tests that we performed (Tajima's D value and Fu's Fs statistics), indicate a recent colonisation event and population growth. Phylogenetic analyses of the COI haplotypes in this study and other T. vaporariorum haplotypes that were retrieved from GenBank were performed using Bayesian inference and median-joining (MJ) network analysis. Two major haplogroups with only a single unique nucleotide difference were found: haplogroup 1 (containing the five Serbian haplotypes and those previously identified in India, China, the Netherlands, the United Kingdom, Morocco, Reunion and the USA) and haplogroup 3 (containing the single Serbian haplotype H3 and haplotypes from Costa Rica, the USA and Spanish Canary Islands). Collectively, our data indicate a rather limited value of COI as a genetic marker for discrimination between different T. vaporariorum populations in the investigated area. Possible explanations for the observed lack of COI sequence variability, such as specific genetics of biological invasion and/or the influence of bacterial symbionts that manipulate insect reproduction, are discussed.

Phylogenetic analysis between domestic and wild duck species in Korea using mtDNA d-loop sequences

Recently, the consumption of duck meat has increased; therefore, we need to reveal the origin and gene flow of domestic ducks in Korea. In order to discriminate between duck species, D-loop variations in mitochondrial DNA (mtDNA) have been investigated. In this study, 45 individuals from seven species of wild and domestic ducks in Korea were considered for the D-loop region sequences. With the participation of all the sequences, a phylogenetic neighbor-joining tree was constructed to differentiate between the wild and domestic duck species. In consideration of these sequences, a total 66 haplotypes were obtained (indel included) with an average haplotype of 76.9%, and a haplotype and nucleotide diversity of 0.91 and 0.01, respectively. Also, an estimation of the sequence divergence within and between species was measured in 0.045 and 0.013-0.095, respectively. Meanwhile, the lowest distances of 0.024, 0.013 and 0.018 were observed in three species, including the Mallard, Spot-billed and domestic duck, respectively, which have relatively close genetic relationships. All haplotypes were used for the median-joining network analysis to differentiate all duck species, while three duck species were closely related. Moreover, 26 indel polymorphisms were identified which could be used for the discrimination among the duck species. Based on our results, duck species were effectively discriminated in a D-loop region, which could then be used for an appropriate genetic conservation program for the wild duck and domestic duck breeds in Korea.

Preliminary study of the genetic diversity of eastern Assamese macaques (Macaca assamensis assamensis) in Thailand based on mitochondrial DNA and microsatellite markers

Human overpopulation, deforestation, invasion of agricultural areas, and livestock are the primary causes for population fragmentation of wildlife. The distribution range of species of the genus Macaca is constantly decreasing and becoming increasingly fragmented due to forest deterioration. Assamese macaques (M. assamensis) are classified as near threatened in the International Union for Conservation of Nature (IUCN) Red List of Threatened Animals (2008) and have been declared a protected wildlife animal according to Wildlife Preservation and Protection Act, B.E.2535 (1992) of Thailand. As studies of the population history and genetic diversity of Assamese macaques in Thailand are currently lacking, we aimed at a first investigation of their genetic diversity based on mitochondrial DNA [hypervariable regions 1 and 2 (HV1, HV2) and cytochrome B (CYTB) regions], as well as 15 microsatellite markers of five sampling sites distributed across Thailand. Our results indicate that Assamese macaques in Thailand are diverse, with eight maternal haplotypes and a low inbreeding coefficient in the Phu Khieo Wildlife Sanctuary (PKWS) population. Moreover, our phylogenetic and median-joining network analysis based on mitochondrial (mt)DNA suggests a population distribution in accordance with the evolutionary scenario proposed for M. sinica. Today, the population of Assamese macaques is fragmented, and conservation strategies are needed to ensure the maintenance of genetic diversity of this primate species.

Evolutionary perspective on hepatitis B virus with an expanded sampling strategy

To investigate the role hepatitis B e antigen (HBeAg) plays in the evolution of hepatitis B virus (HBV), we sequenced the basic core promoter (BCP) and precore (preC) regions of 348 clones total from ten HBV Chinese patients. Eleven mutations were more frequent in HBeAg-negative patients than in HBeAg-positive patients. Further, the sequencing of dozens of variants was found to be necessary to obtain mutation profiles. Phylogenetic and median-joining network analyses suggested that variants from each patient had a single common ancestor (monophyly). Higher haplotype and nucleotide diversities were identified in HBeAg-negative patients. Analysis of dN/dS suggested that viruses experiencing a stronger immune response had lower haplotype diversity. Because HBeAg seroconversion was associated with viral diversity it served as an indicator of HBV evolution. Significantly, this study indicated a larger sampling of variants from each patient was required to understand effectively the properties of HBV.

Genetic diversity and population structure of silver pomfret (Pampus argenteus) in the Indo-West Pacific revealed by mitochondrial control region sequences

Sequence variation of the mitochondrial control region in silver pomfret (Pampus argenteus) among six populations from the Indo-West Pacific region was analyzed. A total of 309 polymorphic sites were detected in the 464–466 bp segment of the control region among 165 individuals which defined 72 haplotypes. Haplotype diversity was ranged from 0.800 to 0.943 and nucleotide diversity ranged from 0.333% to 1.886%. Genetic distance and the fixation index indicated significant differences among populations in different geographical groups (P < 0.05). Median-joining network analysis data showed distinct patterns of phylogeographic structure. The present results suggested that P. argenteus populations have developed significant genetic structure, especially among geographically isolated groups.

Tick-borne Encephalitis Virus, Zealand, Denmark, 2011

Tick-borne Encephalitis Virus, Zealand, Denmark, 2011

Genetic characterization of Clupisoma garua (Hamilton 1822) from six Indian populations using mtDNA cytochrome b gene

Clupisoma garua (Hamilton, 1822) is a commercially important freshwater fish and a potential candidate species for aquaculture. This study investigates the genetic diversity and population structure of six Indian populations of C. garua using cytochrome b (cyt b) sequences of mitochondrial DNA (mtDNA). We sequenced cyt b gene of 64 individuals collected from five distant rivers: Ganga, Gomti, Betwa, Gandak and Brahmaputra. Sequencing of 1054 bp cyt b mtDNA fragment revealed the presence of 19 haplotypes with a haplotype diversity value of 1.000 and a nucleotide diversity value of 0.0258 ± 0.00164. The Gandak river fish population showed highest nucleotide diversity. The fixation index analysis indicated significant genetic divergence among populations from different geographical areas. Both the neighbor-joining tree and median-joining network analysis of the haplotype data showed distinct patterns of phylo-geographic structure. The hierarchical analysis of molecular variance revealed that intra-group variation among populations was highly significant. The results of this study suggest that C. garua populations, especially geographically isolated groups, have developed significant genetic structures within the population. In addition, tests of neutrality suggest that C. garua may have experienced a population expansion. The study results establish cyt b as polymorphic and a potential marker to determine the population structure of C. garua. Information of genetic variation and population structure generated from this study would be useful for planning effective strategies for the conservation and rehabilitation of Schilibid cat fishes.

Reticulate evolution in Ranunculus cantonensis polyploid complex and its allied species

Hybridization is particularly likely to occur in initial and young polyploid complexes, and interspecies hybridization between diverged species usually leads to a complicated reticulate evolution. The Ranunculus cantoniensis complex and its allied species include R. chinensis (2x), R. silerifolius var. silerifolius (2x), R. cantoniensis (4x), R. trigonus (2x), R. shuichengensis (2x), R. diffusus (4x), R. repens (4x), R. vaginatus (5x) and R. sieboldii (6x, 8x). Many morphological intermediates can be found between the members of this complex, and the relationship among members is complicated. By analyzing internal transcribed spacers and nrDNA FISH (fluorescence in situ hybridization) signals, we unraveled the phylogenetic and genetic constitution of the various taxonomic units of this complex. Haplotypes were highly separated by median-joining network analysis and at least four haplogroups emerged in which there were 11 primary haplotypes; six out of ten taxa shared haplotype 1, suggesting that haplotype 1, a variation of the primary haplotype R. chinensis, served as the pivotal genome in the complex. The pollen characteristics and electrophoretic patterns of R. vaginatus (5x) showed it to be an intermediate between R. diffusus (4x) and R. sieboldii (6x). The distribution of R. vaginatus (5x) was located at the junction of the distributions of R. diffusus (4x) and R. sieboldii (6x). Ranunculus vaginatus (5x) shared haplotypes 7 and 8 with R. diffusus (4x), and haplotypes 8 and 9 with R. sieboldii (6x). This proved that R. vaginatus (5x) emerged from hybridization between R. diffusus (4x) and R. sieboldii (6x). The results of FISH also support a hybrid origin of R. vaginatus (5x). The findings of this study clearly show that there are only eight taxa in this polyploid complex including R. chinensis (2x), R. silerifolius var. silerifolius (2x), R. trigonus (2x), R. silerifolius var. dolicanthus(2x), R. cantoniensis (4x), R. diffusus (2x), R. vaginatus (5x) and R. sieboldii (6x, 8x). These taxa associated with each other by hybridizing with the pivotal genome. Ranunculus cantoniensis (4x) and R. vaginatus (5x) arose from hybridization events between diverged species in the polyploid complex, leading to a complicated reticulate evolution.

Continental phylogeography of an ecologically and morphologically diverse Neotropical songbird, Zonotrichia capensis.

BackgroundThe Neotropics are exceptionally diverse, containing roughly one third of all extant bird species on Earth. This remarkable species richness is thought to be a consequence of processes associated with both Andean orogenesis throughout the Tertiary, and climatic fluctuations during the Quaternary. Phylogeographic studies allow insights into how such events might have influenced evolutionary trajectories of species and ultimately contribute to a better understanding of speciation. Studies on continentally distributed species are of particular interest because different populations of such taxa may show genetic signatures of events that impacted the continent-wide biota. Here we evaluate the genealogical history of one of the world’s most broadly-distributed and polytypic passerines, the rufous-collared sparrow (Zonotrichia capensis).ResultsWe obtained control region DNA sequences from 92 Zonotrichia capensis individuals sampled across the species’ range (Central and South America). Six additional molecular markers, both nuclear and mitochondrial, were sequenced for a subset of individuals with divergent control region haplotypes. Median-joining network analysis, and Bayesian and maximum parsimony phylogenetic analyses all recovered three lineages: one spanning Middle America, the Dominican Republic, and north-western South America; one encompassing the Dominican Republic, Roraima (Venezuela) and La Paz (Bolivia) south to Tierra del Fuego, Argentina; and a third, including eastern Argentina and Brazil. Phylogenetic analyses suggest that the Middle American/north-western South American clade is sister to the remaining two. Bayesian and maximum likelihood coalescent simulations used to study lineage demographic history, diversification times, migration rates and population expansion together suggested that diversification of the three lineages occurred rapidly during the Pleistocene, with negligible gene flow, leaving genetic signatures of population expansions.ConclusionsThe Pleistocene history of the rufous-collared sparrow involved extensive range expansion from a probable Central American origin. Its remarkable morphological and behavioral diversity probably represents recent responses to local conditions overlying deeper patterns of lineage diversity, which are themselves produced by isolation and the history of colonization of South America.

Genetic variation of the Chinese longsnout catfish Leiocassis longirostris in the Yangtze River revealed using mitochondrial DNA cytochrome b sequences

The mitochondrial DNA cytochrome b of 132 Leiocassis longirostris collected from 12 localities in the upper to lower reaches of the Yangtze River were amplified and partially sequenced using the PCR technique. The results showed that 27 nucleotide sites were variable along 817bp length of homologous sequence (3.3%), base substitutions happened mostly at the third codon position. A total of 22 haplotypes were identified, which were characterized with moderate haplotype diversity (h=0.5417±0.0519), but low nucleotide diversity (π=0.0019±0.0012). Median-joining network analysis revealed star-shaped patterns with one common central haplotype (H3), whereas mismatch distribution analysis found that the Chinese longsnout catfish fitted a smooth unimodal distribution, which suggested that this species underwent population expansion following bottlenecks and/or they originated from a small number of founding individuals. The time that the total population of Chinese longsnout catfish in the Yangtze River expanded was estimated 169,000–337,000years before present. The analysis of molecular variance (AMOVA) and phylogenetic reconstructions did not detect significant geographic structure between different river sections, especially between above and below the Gezhouba Dam and the Three Gorges Dam, which suggested that these recently developed dams might have not significantly resulted in population genetic differentiation in the Chinese longsnout catfish.

Phylogenetic relationship and species delimitation of matsutake and allied species based on multilocus phylogeny and haplotype analyses

Tricholoma matsutake (S. Ito & S. Imai) Singer and its allied species are referred to as matsutake worldwide and are the most economically important edible mushrooms in Japan. They are widely distributed in the northern hemisphere and established an ectomycorrhizal relationship with conifer and broadleaf trees. To clarify relationships among T. matsutake and its allies, and to delimit phylogenetic species, we analyzed multilocus datasets (ITS, megB1, tef, gpd) with samples that were correctly identified based on morphological characteristics. Phylogenetic analyses clearly identified four major groups: matsutake, T. bakamatsutake, T. fulvocastaneum and T. caligatum; the latter three species were outside the matsutake group. The haplotype analyses and median-joining haplotype network analyses showed that the matsutake group included four closely related but clearly distinct taxa (T. matsutake, T. anatolicum, Tricholoma sp. from Mexico and T. magnivelare) from different geographical regions; these were considered to be distinct phylogenetic species.

Fungal-algal interactions inRamalina menziesiiand its associated epiphytic lichen community

AbstractLichens are a fascinating example of a symbiotic mutualism. It is still uncertain which processes guide fungal-photobiont interactions, and whether they are random or of a more complex nature. Here, the fungal-algal interactions inRamalina menziesiiand co-occurring taxa are analyzed by using DNA sequences of the algal Internal Transcribed Spacer region (ITS), to investigate fungal-algal associations in juvenileR. menziesiiand allied species. Algal species were identified by a combination of BLAST searches, median-joining network analysis, and Bayesian phylogenetics. Fungal-algal networks were analyzed for nestedness, both at the species and haplotype level (fungal species vs. algal haplotypes), and the networks were inspected for evidence of compartmentalization. Bayesian phylogenetic trees indicated that the widespread green algaTrebouxia decoloransassociated withR. menziesii, as well as six other fungal species. Four additional fungal species interacted with four different species ofTrebouxia. Only in one out of ten samples were algal haplotypes shared with the nearest neighbours of juvenileR. menziesii. Fungal-algal species interactions were compartmentalized, while at the level of algal haplotypes, nestedness was found. This pattern is similar to the compartmentalization found in other intimately interacting mutualists.