Koorchaloma oryzae sp. nov. (Stachybotryaceae, Sordariomycetes), from Oryza sativa (Poaceae) in northern Thailand

A new species of Koorchaloma is described based on morphology and multigene phylogenetic analyses of ITS, LSU and RPB2. Phylogenetic analyses showed our strain clusters with K. europaea with moderate statistical support. Koorchaloma oryzae sp. nov. is morphologically similar to K. europaea, but it can be distinguished by the conidiophores and conidia, while ITS pairwise nucleotide comparison of these two species also revealed differences. Koorchaloma oryzae is compared with all known Koorchaloma species, and a key to Koorchaloma species is provided. Genealogical concordance phylogenetic species recognition analysis (PHI test) results of the new species and closely related species are also given.

Phylogeography of southern New Zealand: Implications of Pliocene and Pleistocene Processes and Evolutionary Concordance Across Independent Loci

<p>The endemic fauna of the South Island has proven to be an ideal taxonomic group to examine the impact of climatic and geological processes on the evolution of New Zealand's biota since the Pliocene. This thesis examines the phylogeography of McCann's skink (Oligosoma maccanni) in order to provide insight into the relative contribution of Pliocene and Pleistocene processes on patterns of genetic structure in South Island biota. This thesis also investigates the phylogeography of the brown skink (O. zelandicum) to examine whether Cook Strait landbridges facilitated gene flow between the North and South Island in the late-Pleistocene. This thesis also investigates the presence of genealogical concordance across independent loci for the endemic alpine stick insect, Niveaphasma. I obtained mitochondrial DNA (mtDNA) sequence data (ND2 and ND4; 1284 bp) from across the range of both skink species and mtDNA (COI; 762 bp) and nuclear sequence data (EF1 ; 590 bp) from across the range of Niveaphasma. I used DGGE in order to resolve nuclear EF1 alleles and examined phylogeographic patterns in each species using Neighbour-Joining, Maximum Likelihood and Bayesian methods. Substantial phylogeographic structure was found within O. maccanni, with divergences among clades estimated to have occurred during the Pliocene. Populations in the Otago/Southland region formed a well-supported lineage within O. maccanni. A genetic break was evident between populations in east and west Otago, while north-south genetic breaks were evident within the Canterbury region. There was relatively minor phylogeographic structure within O. zelandicum. Our genetic data supports a single colonization of the North Island by O. zelandicum from the South Island, with the estimated timing of this event (0.46 Mya) consistent with the initial formation of Cook Strait. There was substantial genetic structuring identified within Niveaphasma, with a well-supported lineage present in the Otago/Southland region. There was also a genetic break between populations in Canterbury and eastern Otago with those in central Otago and Southland. The genetic data provided strong genealogical concordance between mtDNA haplotypes and nuclear alleles suggesting an accurate depiction of the historical isolation identified between the major clades of Niveaphasma. This finding offers compelling evidence for the use of nuclear gene phylogeography alongside mtDNA for future evolutionary studies within New Zealand.</p>

Phylogeography of southern New Zealand: Implications of Pliocene and Pleistocene Processes and Evolutionary Concordance Across Independent Loci

<p>The endemic fauna of the South Island has proven to be an ideal taxonomic group to examine the impact of climatic and geological processes on the evolution of New Zealand's biota since the Pliocene. This thesis examines the phylogeography of McCann's skink (Oligosoma maccanni) in order to provide insight into the relative contribution of Pliocene and Pleistocene processes on patterns of genetic structure in South Island biota. This thesis also investigates the phylogeography of the brown skink (O. zelandicum) to examine whether Cook Strait landbridges facilitated gene flow between the North and South Island in the late-Pleistocene. This thesis also investigates the presence of genealogical concordance across independent loci for the endemic alpine stick insect, Niveaphasma. I obtained mitochondrial DNA (mtDNA) sequence data (ND2 and ND4; 1284 bp) from across the range of both skink species and mtDNA (COI; 762 bp) and nuclear sequence data (EF1 ; 590 bp) from across the range of Niveaphasma. I used DGGE in order to resolve nuclear EF1 alleles and examined phylogeographic patterns in each species using Neighbour-Joining, Maximum Likelihood and Bayesian methods. Substantial phylogeographic structure was found within O. maccanni, with divergences among clades estimated to have occurred during the Pliocene. Populations in the Otago/Southland region formed a well-supported lineage within O. maccanni. A genetic break was evident between populations in east and west Otago, while north-south genetic breaks were evident within the Canterbury region. There was relatively minor phylogeographic structure within O. zelandicum. Our genetic data supports a single colonization of the North Island by O. zelandicum from the South Island, with the estimated timing of this event (0.46 Mya) consistent with the initial formation of Cook Strait. There was substantial genetic structuring identified within Niveaphasma, with a well-supported lineage present in the Otago/Southland region. There was also a genetic break between populations in Canterbury and eastern Otago with those in central Otago and Southland. The genetic data provided strong genealogical concordance between mtDNA haplotypes and nuclear alleles suggesting an accurate depiction of the historical isolation identified between the major clades of Niveaphasma. This finding offers compelling evidence for the use of nuclear gene phylogeography alongside mtDNA for future evolutionary studies within New Zealand.</p>

Parallel introgression, not recurrent emergence, explains apparent elevational ecotypes of polyploid Himalayan snowtrout

The recurrence of similar evolutionary patterns within different habitats often reflects parallel selective pressures acting upon either standing or independently occurring genetic variation to produce a convergence of phenotypes. This interpretation (i.e. parallel divergences within adjacent streams) has been hypothesized for drainage-specific morphological ‘ecotypes’ observed in polyploid snowtrout (Cyprinidae: Schizothorax ). However, parallel patterns of differential introgression during secondary contact are a viable alternative hypothesis. Here, we used ddRADseq ( N = 35 319 de novo and N = 10 884 transcriptome-aligned SNPs), as derived from Nepali/Bhutanese samples ( N = 48 each), to test these competing hypotheses. We first employed genome-wide allelic depths to derive appropriate ploidy models, then a Bayesian approach to yield genotypes statistically consistent under the inferred expectations. Elevational ‘ecotypes’ were consistent in geometric morphometric space, but with phylogenetic relationships at the drainage level, sustaining a hypothesis of independent emergence. However, partitioned analyses of phylogeny and admixture identified subsets of loci under selection that retained genealogical concordance with morphology, suggesting instead that apparent patterns of morphological/phylogenetic discordance are driven by widespread genomic homogenization. Here, admixture occurring in secondary contact effectively ‘masks’ previous isolation. Our results underscore two salient factors: (i) morphological adaptations are retained despite hybridization and (ii) the degree of admixture varies across tributaries, presumably concomitant with underlying environmental or anthropogenic factors.

Genealogical concordance of phylogenetic species recognition-based delimitation of Neopestalotiopsis species associated with leaf spots and fruit canker disease affected guava plants

Neopestalotiopsis species are known to be involved in plant diseases as associated pathogens. The taxonomic identification of the fungal group Neopestalotiopsisis little bit difficult due to its complex evolutionary history. In the present study, seven fungal isolates were investigated from canker-affected guava plants. The phylogeny for generic placement of these isolates was analyzed to validate them as Neopestalotiopsis genus by phylogenetic signals from the 28S nrRNA region (LSU). Generated morphological data was segregated as new morpho-species of the Neopestalotiopsis genus. Hence, the internal transcribed spacer (ITS), Translation elongation factor 1-α (TEF1-α) and Tubulin (TUB) genic region of these isolates were studied in juxtaposition with morphological data to resolve species limits. Both phylogenetic and morphological data revealed four novel species of the Neopestalotiopsis genus out of seven isolates studied. These Neopestalotiopsis species could be of great significance for further investigation as putative pathogens associated with canker or scabby canker disease in guava.

First report of Head blight of wheat caused by Fusarium vorosii in Serbia

The cosmopolitan species Fusarium graminearum Schwabe directly reduces yield, as well as grain quality of cereals, due to its ability to synthesize mycotoxins. Previously it was considered to be one species occurring on all continents. However, phylogenetic analysis employing the GCPSR method (Genealogical Concordance Phylogenetic Species Recognition) revealed the existence of 15 phylogenetic species within what is now recognised as the Fusarium graminearum Species Complex (FGSC) (Sarver et al. 2011). During 1996-2008, a MRIZP collection of FGSC isolates was established and isolates originating from wheat (5), maize (3) and barely (2) were selected for further study. Morphological features including the appearance of colonies and macroconidia (average size 38.5-53.1 × 4.6-5.4 µm, No 50) of all 10 isolates on PDA were consistent with descriptions of F. graminearum (O’Donnell et al. 2004, Leslie and Summerell 2006). Total DNA was isolated from mycelium removed from 7-day old colonies of single-spore isolates grown on PDA using the DNeasy Plant Mini Kit (Qiagen, Hilden). Further identification was based on amplification and sequencing of elongation factor TEF−1α, histone H3 and β−tubulin in both directions, with primers ef1/ef2, H3-1a/H3-1b and T1/T22, respectively (Jacobs et al. 2010). The sequences were deposited in NCBI under accession numbers MF974399 - MF974408 (TEF−1α), MG063783 - MG063792 (β−tubulin) and MF999139 - MF999148 (histone H3). Sequence analysis was performed using BLAST while genetic similarity was calculated using MEGA 6.0 software. Isolate 1339 originating from wheat (collected at the locality of Kikinda in 2006), shared 100% nucleotide identity with TEF−1α (DQ459745), histone H3 (DQ459728) and β−tubulin (DQ459643) of F. vorosii isolate NRRL37605 (Starkey et al. 2007). The remaining nine isolates were identified as F. graminearum as they shared 99% to 100% nucleotide similarity with F. graminearum NRRL 28439 (O’Donnell et al. 2004). Pathogenicity was tested using artificial inoculations of spikes during wheat flowering (Mesterhazy et al. 1999). Thirty classes were inoculated with each isolate, in three replicates. Inoculum was prepared from 7-day colonies on PDA, and 30 ml of a conidia suspension (1x105 conidia/ml) was used. Control plants were inoculated with sterile water. Three weeks after inoculation, typical Fusarium head blight symptoms were visible on inoculated plants, from which all 10 isolates were successfully reisolated. Control spikes remained symptomless. Disease severity was estimated on the 1-7 scale (Blandino et al. 2012). Average pathogenicity of the F. vorosii isolate 1339 was 1.9, and 2.4 -5.1 of F. graminearum isolates. Toxin production was determined using gas chromatography-tandem mass spectrometry. Kernels inoculated with the 10 isolates were ground and tested for the presence of deoxynivalenol (DON) and its acetyl derivatives 3ADON, 15ADON and NIV. F. vorosii isolate 1339 possessed the 15ADON chemotype, as well as eight F. graminearum isolates, while only one F. graminearum isolate was 3ADON chemotype. To date, F. vorosii has only been detected in Hungary on wheat (Toth et al. 2005) and Korea on barley, corn and rice (Lee et al. 2016). This is the first report of F. vorosii in Serbia, which is of great importance, because it indicates the spread of this toxigenic species. Further studies should be focused on determining the distribution, aggressiveness and toxicological profile of F. vorosii.

Using Genealogical Concordance and Coalescent-Based Species Delimitation to Assess Species Boundaries in the Diaporthe eres Complex

DNA sequence analysis has been of the utmost importance to delimit species boundaries in the genus Diaporthe. However, the common practice of combining multiple genes, without applying the genealogical concordance criterion has complicated the robust delimitation of species, given that phylogenetic incongruence between loci has been disregarded. Despite the several attempts to delineate the species boundaries in the D. eres complex, the phylogenetic limits within this complex remain unclear. In order to bridge this gap, we employed the Genealogical Phylogenetic Species Recognition principle (GCPSR) and the coalescent-based model Poisson Tree Processes (PTPs) and evaluated the presence of recombination within the D. eres complex. Based on the GCPSR principle, presence of incongruence between individual gene genealogies, i.e., conflicting nodes and branches lacking phylogenetic support, was evident. Moreover, the results of the coalescent model identified D. eres complex as a single species, which was not consistent with the current large number of species within the complex recognized in phylogenetic analyses. The absence of reproductive isolation and barriers to gene flow as well as the high haplotype and low nucleotide diversity indices within the above-mentioned complex suggest that D. eres constitutes a population rather than different lineages. Therefore, we argue that a cohesive approach comprising genealogical concordance criteria and methods to detect recombination must be implemented in future studies to circumscribe species in the genus Diaporthe.

Molecular and Morphological Assessment of Septoria Species Associated with Ornamental Plants in Yunnan Province, China

The Karst landform is the main geographic characteristic in South China. Such areas are rich in vegetation and especially suitable for growth of shrubs and herbaceous plants. In this study, 11 Septoria strains were obtained from different plants’ leaves collected in the Kunming Botanical Garden, Yunnan Province, China. Based on single-gene and multi-gene analyses of five gene loci (tef1, rpb2, tub2, ITS, and LSU) and four gene regions (without LSU), these strains were found to belong to three independent phylogenetic lineages representing five species, including four novel taxa, and one new record for China. Five single gene trees were also provided to evaluate the effectiveness of each gene for discriminating the species, as a result of which tub2 was found to have the most suitable DNA barcode for rapid identification. Morphological descriptions, illustrations, and comparisons are provided for a more comprehensive assessment. Genealogical Concordance Phylogenetic Species Recognition (GCPSR) with a pairwise homoplasy index (PHI) test was used to evaluate the conclusions of the phylogenetic analyses.

Parallel adaptations to an altitudinal gradient persist in tetraploid snowtrout (Cyprinidae: Schizothorax), despite extensive genomic exchange within adjacent Himalayan rivers

Replicated evolutionary patterns are often attributed to recurrent emergence following parallel selective pressures. However, similar genetic patterns (e.g., 'genomic islands') can also emerge following extensive homogenization in secondary contact, as a by-product of heterogeneous introgression. For example, within Himalayan tributaries of the Ganges/Brahmaputra rivers, drainage-specific mtDNA clades of polyploid snowtrout (Cyprinidae: Schizothorax) are partitioned as co-occurring morphological 'ecotypes,' hypothesized to represent parallel divergence among adjacent streams. To evaluate this scenario, we utilized a reduced-representation genomic approach (N=35,319 de-novo and N=10,884 transcriptome-aligned SNPs) applied to high-altitude Nepali/Bhutanese snowtrout (N=48 each). We unambiguously quantified ploidy levels by first deriving genome-wide allelic depths followed by ploidy-aware Bayesian models that produced genotypes statistically consistent with diploid/tetraploid expectations. When genotyped SNPs were clustering within drainages, the convergence of eco-phenotypes was sustained. However, subsequent partitioned analyses of phylogeny and population admixture instead identified subsets of loci under selection which retained genealogical concordance with morphology, with apparent patterns of parallel ecotype emergence instead driven by widespread genomic homogenization. Here, prior isolation is effectively masked by admixture occurring in secondary contact. We note two salient factors:1) Polyploidy has promoted homogenization in tetraploid Himalayan snowtrout; and 2) Homogenization varies across Himalayan tributaries, presumably in lockstep with extent of anthropogenic modification.