Publications by authors named "Ekaphan Kraichak"

20 Publications

  • Page 1 of 1

Comparative anatomy and salt management of (L.) Engl. (Lythraceae) grown in saltwater and freshwater.

PeerJ 2021 25;9:e10962. Epub 2021 Feb 25.

Department of Botany, Faculty of Science, Kasetsart University, Bangkok, Thailand.

is a pioneer species in mangrove. It can naturally grow in both saltwater and freshwater. The study was aimed at investigating and comparing the anatomical character of the plants growing in different conditions and how they coped with salinity. The anatomical characteristics of roots, stems, petioles and leaf blade were investigated. The plant samples were prepared into permanent slides using a paraffin method, while the wood samples were made into permanent slides using a sliding microtome technique. Tissue clearing of leaf blade and scanning electron microscopic analysis of wood were performed. In addition, sodium chloride content in various organs and tissues was examined. It was found that cable root, stem and leaf blade showed some different anatomical characteristics between the two conditions. Periderm is a prominent tissue in saltwater roots. Tanniferous cells were observed in pneumatophores, petioles, stems and leaf blades of saltwater plants, but not found in pneumatophores and lamina of freshwater plants. Mesophyll thickness was lower in the saltwater condition. The vessel density was significantly higher in the saltwater condition than in the freshwater condition, whereas the vessel diameters in the freshwater condition were significantly higher than those in the saltwater condition. From the results, it can be concluded that root periderm plays an important role in salt exclusion, and the occurrence of tanniferous cells is associated with salt elimination.
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http://dx.doi.org/10.7717/peerj.10962DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7916540PMC
February 2021

An Investigation of ZZ/ZW and XX/XY Sex Determination Systems in North African Catfish (, ).

Front Genet 2020 5;11:562856. Epub 2021 Jan 5.

Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.

An investigation of sex-specific loci may provide important insights into fish sex determination strategies. This may be useful for biotechnological purposes, for example, to produce all-male or all-female fish for commercial breeding. The North African catfish species, , has been widely adopted for aquaculture because its superior growth and disease resistance render the species suitable for hybridization with other catfish to improve the productivity and quality of fish meat. This species has either a ZZ/ZW or XX/XY sex determination system. Here, we investigate and characterize these systems using high-throughput genome complexity reduction sequencing as Diversity Arrays Technology. This approach was effective in identifying moderately sex-linked loci with both single-nucleotide polymorphisms (SNPs) and restriction fragment presence/absence (PA) markers in 30 perfectly sexed individuals of . However, SNPs based markers were not found in this study. In total, 41 loci met the criteria for being moderately male-linked (with male vs. female ratios 80:20 and 70:30), while 25 loci were found to be moderately linked to female sex. No strictly male- or female-linked loci were detected. Seven moderately male-linked loci were partially homologous to some classes of transposable elements and three moderately male-linked loci were partially homologous to functional genes. Our data showed that the male heterogametic XX/XY sex determination system should co-exist with the ZZ/ZW system in . Our finding of the co-existence of XX/XY and ZZ/ZW systems can be applied to benefit commercial breeding of this species in Thailand. This approach using moderately sex-linked loci provides a solid baseline for revealing sex determination mechanisms and identify potential sex determination regions in catfish, allowing further investigation of genetic improvements in breeding programs.
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http://dx.doi.org/10.3389/fgene.2020.562856DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7874028PMC
January 2021

Genome Complexity Reduction High-Throughput Genome Sequencing of Green Iguana () Reveal a Paradigm Shift in Understanding Sex-Chromosomal Linkages on Homomorphic X and Y Sex Chromosomes.

Front Genet 2020 20;11:556267. Epub 2020 Oct 20.

Laboratory of Animal Cytogenetics and Comparative Genomics, Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.

The majority of lizards classified in the superfamily Iguanoidea have an XX/XY sex-determination system in which sex-chromosomal linkage shows homology with chicken () chromosome 15 (GGA15). However, the genomics of sex chromosomes remain largely unexplored owing to the presence of homomorphic sex chromosomes in majority of the species. Recent advances in high-throughput genome complexity reduction sequencing provide an effective approach to the identification of sex-specific loci with both single-nucleotide polymorphisms (SNPs) and restriction fragment presence/absence (PA), and a better understanding of sex chromosome dynamics in Iguanoidea. In this study, we applied Diversity Arrays Technology (DArTseq) in 29 phenotypic sex assignments (14 males and 15 females) of green iguana (). We confirmed a male heterogametic (XX/XY) sex determination mode in this species, identifying 29 perfectly sex-linked SNP/PA loci and 164 moderately sex-linked SNP/PA loci, providing evidence probably indicative of XY recombination. Three loci from among the perfectly sex-linked SNP/PA loci showed partial homology with several amniote sex chromosomal linkages. The results support the hypothesis of an ancestral super-sex chromosome with overlaps of partial sex-chromosomal linkages. However, only one locus among the moderately sex-linked loci showed homology with GGA15, which suggests that the specific region homologous to GGA15 was located outside the non-recombination region but in close proximity to this region of the sex chromosome in green iguana. Therefore, the location of GGA15 might be further from the putative sex-determination locus in green iguana. This is a paradigm shift in understanding linkages on homomorphic X and Y sex chromosomes. The DArTseq platform provides an easy-to-use strategy for future research on the evolution of sex chromosomes in Iguanoidea, particularly for non-model species with homomorphic or highly cryptic sex chromosomes.
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http://dx.doi.org/10.3389/fgene.2020.556267DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7606854PMC
October 2020

Existence of Bov-B LINE Retrotransposons in Snake Lineages Reveals Recent Multiple Horizontal Gene Transfers with Copy Number Variation.

Genes (Basel) 2020 10 22;11(11). Epub 2020 Oct 22.

Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand.

Transposable elements (TEs) are dynamic elements present in all eukaryotic genomes. They can "jump" and amplify within the genome and promote segmental genome rearrangements on both autosomes and sex chromosomes by disruption of gene structures. The Bovine-B long interspersed nuclear element (Bov-B LINE) is among the most abundant TE-retrotransposon families in vertebrates due to horizontal transfer (HT) among vertebrate lineages. Recent studies have shown multiple HTs or the presence of diverse Bov-B LINE groups in the snake lineage. It is hypothesized that Bov-B LINEs are highly dynamic and that the diversity reflects multiple HTs in snake lineages. Partial sequences of Bov-B LINE from 23 snake species were characterized. Phylogenetic analysis resolved at least two Bov-B LINE groups that might correspond to henophidian and caenophidian snakes; however, the tree topology differed from that based on functional nuclear and mitochondrial gene sequences. Several Bov-B LINEs of snakes showed greater than 80% similarity to sequences obtained from insects, whereas the two Bov-B LINE groups as well as sequences from the same snake species classified in different Bov-B LINE groups showed sequence similarities of less than 80%. Calculation of estimated divergence time and pairwise divergence between all individual Bov-B LINE copies suggest invasion times ranging from 79.19 to 98.8 million years ago in snakes. Accumulation of elements in a lineage-specific fashion ranged from 9 × 10% to 5.63 × 10% per genome. The genomic proportion of Bov-B LINEs varied among snake species but was not directly associated with genome size or invasion time. No differentiation in Bov-B LINE copy number between males and females was observed in any of the snake species examined. Incongruence in tree topology between Bov-B LINEs and other snake phylogenies may reflect past HT events. Sequence divergence of Bov-B LINEs between copies suggests that recent multiple HTs occurred within the same evolutionary timeframe in the snake lineage. The proportion of Bov-B LINEs varies among species, reflecting species specificity in TE invasion. The rapid speciation of snakes, coinciding with Bov-B LINE invasion in snake genomes, leads us to better understand the effect of Bov-B LINEs on snake genome evolution.
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http://dx.doi.org/10.3390/genes11111241DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7716205PMC
October 2020

Genome-wide SNP analysis of Siamese cobra (Naja kaouthia) reveals the molecular basis of transitions between Z and W sex chromosomes and supports the presence of an ancestral super-sex chromosome in amniotes.

Genomics 2021 Jan 28;113(1 Pt 2):624-636. Epub 2020 Sep 28.

Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok 10900, Thailand; Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Kasetsart University, Bangkok 10900, Thailand, (CASTNAR, NRU-KU, Thailand); Center of Excellence on Agricultural Biotechnology (AG-BIO/PERDO-CHE), Bangkok 10900, Thailand; Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand; Amphibian Research Center, Hiroshima University, 1-3-1, Kagamiyama, Higashihiroshima 739-8526, Japan. Electronic address:

Elucidation of the process of sex chromosome differentiation is necessary to understand the dynamics of evolutionary mechanisms in organisms. The W sex chromosome of the Siamese cobra (Naja kaouthia) contains a large number of repeats and shares amniote sex chromosomal linkages. Diversity Arrays Technology provides an effective approach to identify sex-specific loci that are epoch-making, to understand the dynamics of molecular transitions between the Z and W sex chromosomes in a snake lineage. From a total of 543 sex-specific loci, 90 showed partial homology with sex chromosomes of several amniotes and 89 loci were homologous to transposable elements. Two loci were confirmed as W-specific nucleotides after PCR amplification. These loci might result from a sex chromosome differentiation process and involve putative sex-determination regions in the Siamese cobra. Sex-specific loci shared linkage homologies among amniote sex chromosomes, supporting an ancestral super-sex chromosome.
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http://dx.doi.org/10.1016/j.ygeno.2020.09.058DOI Listing
January 2021

Characterization of centromeric satellite DNAs (MALREP) in the Asian swamp eel (Monopterus albus) suggests the possible origin of repeats from transposable elements.

Genomics 2020 09 27;112(5):3097-3107. Epub 2020 May 27.

Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand; Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Kasetsart University, Bangkok 10900, Thailand; Center of Excellence on Agricultural Biotechnology (AG-BIO/PERDO-CHE), Bangkok 10900, Thailand; Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand; Amphibian Research Center, Hiroshima University, 1-3-1, Kagamiyama, Higashihiroshima 739-8526, Japan. Electronic address:

Centromeric satellite DNA (cen-satDNA) sequences of the Asian swamp eel (Monopterus albus) were characterized. Three GC-rich cen-satDNA sequences were detected as a 233 bp MALREP-A and a 293 bp MALREP-B localized to all chromosomes, and a 293 bp MALREP-C distributed on eight chromosome pairs. Sequence lengths of MALREP-B and MALREP-C were 60 bp larger than that of MALREP-A, showing partial homology with core sequences (233 bp). Size differences between MALREP-A and MALREP-B/C suggest the possible occurrence of two satDNA families. The presence of an additional 60 bp in MALREP-B/C resulted from an ancient dimer of 233 bp monomers and subsequent mutation and homogenization between the two monomers. All MALREPs showed partial homology with transposable elements (TEs), suggesting that the MALREPs originated from the TEs. The MALREPs might have been acquired in the Asian swamp eel, thereby promoting fixation in the species.
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http://dx.doi.org/10.1016/j.ygeno.2020.05.024DOI Listing
September 2020

Diversity of PBI-DdeI satellite DNA in snakes correlates with rapid independent evolution and different functional roles.

Sci Rep 2019 10 29;9(1):15459. Epub 2019 Oct 29.

Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand.

To better understand PBI-DdeI satellite DNA located in the centromeric region of python, molecular evolution analysis was conducted on 40 snake species. A ladder-like pattern of DNA bands with repetition of the 194-210 bp monomer was observed in 15 species using PCR. Molecular cloning was performed to obtain 97 AT-rich monomer sequences. Phylogenetic and network analyses showed three PBI-DdeI subfamilies with sequences grouped in species-specific clusters, suggesting rapid evolution. Slow evolution was found in eight species with shared PBI-DdeI sequences, suggesting recent species diversification, allowing PBI-DdeI no time to diverge, with limited homogenization and fixation processes. Quantitative real-time PCR showed large differences in copy number between Python bivittatus and other snakes, consistent with repeat scanning of whole genome sequences. Copy numbers were significantly higher in female Naja kaouthia than in males, concurring with chromosomal distribution of PBI-DdeI specifically localized to female W chromosomes. PBI-DdeI might act as an evolutionary driver with several repeats to promote W chromosome differentiation and heterochromatinization in N. kaouthia. Analysis revealed PBI-DdeI with a reduced copy number, compared to P. bivittatus, in most snakes studied, and it is possible that it subsequently dispersed and amplified on W chromosomes with different functional roles in N. kaouthia.
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http://dx.doi.org/10.1038/s41598-019-51863-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6820872PMC
October 2019

Take one step backward to move forward: Assessment of genetic diversity and population structure of captive Asian woolly-necked storks (Ciconia episcopus).

PLoS One 2019 10;14(10):e0223726. Epub 2019 Oct 10.

Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.

The fragmentation of habitats and hunting have impacted the Asian woolly-necked stork (Ciconia episcopus), leading to a serious risk of extinction in Thailand. Programs of active captive breeding, together with careful genetic monitoring, can play an important role in facilitating the creation of source populations with genetic variability to aid the recovery of endangered species. Here, the genetic diversity and population structure of 86 Asian woolly-necked storks from three captive breeding programs [Khao Kheow Open Zoo (KKOZ) comprising 68 individuals, Nakhon Ratchasima Zoo (NRZ) comprising 16 individuals, and Dusit Zoo (DSZ) comprising 2 individuals] were analyzed using 13 microsatellite loci, to aid effective conservation management. Inbreeding and an extremely low effective population size (Ne) were found in the KKOZ population, suggesting that deleterious genetic issues had resulted from multiple generations held in captivity. By contrast, a recent demographic bottleneck was observed in the population at NRZ, where the ratio of Ne to abundance (N) was greater than 1. Clustering analysis also showed that one subdivision of the KKOZ population shared allelic variability with the NRZ population. This suggests that genetic drift, with a possible recent and mixed origin, occurred in the initial NRZ population, indicating historical transfer between captivities. These captive stork populations require improved genetic variability and a greater population size, which could be achieved by choosing low-related individuals for future transfers to increase the adaptive potential of reintroduced populations. Forward-in-time simulations such as those described herein constitute the first step in establishing an appropriate source population using a scientifically managed perspective for an in situ and ex situ conservation program in Thailand.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0223726PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6786576PMC
March 2020

Accelerated diversifications in three diverse families of morphologically complex lichen-forming fungi link to major historical events.

Sci Rep 2019 06 28;9(1):8518. Epub 2019 Jun 28.

Integrative Research Center, The Field Museum, Chicago, IL, 60605, USA.

Historical mass extinction events had major impacts on biodiversity patterns. The most recent and intensively studied event is the Cretaceous - Paleogene (K-Pg) boundary (ca. 66 million years ago [MYA]). However, the factors that may have impacted diversification dynamics vary across lineages. We investigated the macroevolutionary dynamics with a specific focus on the impact of major historical events such as the K-Pg mass extinction event on two major subclasses - Lecanoromycetidae and Ostropomycetidae - of lichen-forming fungi and tested whether variation in the rate of diversification can be associated with the evolution of a specific trait state - macrolichen. Our results reveal accelerated diversification events in three families of morphologically complex lichen-forming fungi - Cladoniaceae, Parmeliaceae, and Peltigeraceae - which are from the subclass Lecanoromycetidae and mostly composed of macrolichens, those that form three dimensional structures. Our RTT plot result for the subclass Lecanoromycetidae also reveals accelerated diversification. Changes in diversification rates occurred around the transition between Mesozoic and Cenozoic eras and was likely related to the K-Pg mass extinction event. The phylogenetic positions for rate increases estimated based on marginal shift probability are, however, scattered from 100 to 40 MYA preventing us from making explicit inference. Although we reveal that the phenotypic state of macrolichens is associated with a higher diversification rate than microlichens, we also show that the evolution of macrolichens predated the K-Pg event. Furthermore, the association between macrolichens and increased diversification is not universal and can be explained, in part, by phylogenetic relatedness. By investigating the macroevolutionary dynamics of lichen-forming fungi our study provides a new empirical system suitable to test the effect of major historical event on shaping biodiversity patterns and to investigate why changes in biodiversity patterns are not in concordance across clades. Our results imply that multiple historical events during the transition from Mesozoic to Cenozoic eras, including the K-Pg mass extinction event, impacted the evolutionary dynamics in lichen-forming fungi. However, future studies focusing on individual lichen-forming fungal families are required to ascertain whether diversification rates are associated with growth form and certain geological events.
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http://dx.doi.org/10.1038/s41598-019-44881-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6599062PMC
June 2019

Dynamics of telomere length in captive Siamese cobra () related to age and sex.

Ecol Evol 2019 Jun 29;9(11):6366-6377. Epub 2019 Apr 29.

Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics Faculty of Science Kasetsart University Bangkok Thailand.

Telomeres comprise tandem repeated DNA sequences that protect the ends of chromosomes from deterioration or fusion with neighboring chromosomes, and their lengths might vary with sex and age. Here, age- and sex-related telomere lengths in male and female captive Siamese cobras () were investigated using quantitative real-time polymerase chain reaction based on cross-sectional data. A negative correlation was shown between telomere length and body size in males but not in females. Age-related sex differences were also recorded. Juvenile female snakes have shorter telomeres relative to males at up to 5 years of age, while body size also rapidly increases during this period. This suggests that an accelerated increase in telomere length of female cobra results from sex hormone stimulation to telomerase activity, reflecting sexually dimorphic phenotypic traits. This might also result from amplification of telomeric repeats on sex chromosomes. By contrast, female Siamese cobras older than 5 years had longer telomeres than males. Diverse sex hormone levels and oxidative stress parameters between sexes may affect telomere length.
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http://dx.doi.org/10.1002/ece3.5208DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6580288PMC
June 2019

Chemovariation and antibacterial activity of extracts and isolated compounds from species of and (Ixoroideae, Rubiaceae).

PeerJ 2019 7;7:e6893. Epub 2019 May 7.

Department of Botany, Faculty of Science, Kasetsart University, Bangkok, Thailand.

Background: A large number of secondary metabolites can be obtained from plants used for traditional medicine in two related genera ( and ) in the subfamily Ixoroideae (Rubiaceae), but there are only a few detailed studies on their bioactivities. Therefore, the main goals of this study were to determine the antibacterial activities of lipophilic extracts from plants of some and species native to Thailand, and to isolate some pure compounds from those extracts. Moreover, we compared the occurrence of compounds in different plant parts of samples from different habitats to better understand their variation.

Methods: A total of 56 lipophilic extracts were obtained from the leaves, stem bark, and root bark of eight and two species collected at various locations in Thailand. Isolated compounds were identified using nuclear magnetic resonance. Antimicrobial activities were evaluated against four Gram-positive and nine Gram-negative human pathogenic bacterial strains.

Results: Extracts from , along with isolated scopoletin, exhibited antibacterial activities against Gram-positive methicillin-resistant ATCC 43300, with minimum inhibitory concentration values ranging from 64 to 256 µg/mL. The occurrence of scopoletin, isofraxidin, and geniposidic acid in lipophilic extracts showed some variation among different plant parts and species.

Conclusions: Lipophilic extracts of and species have the potential to be developed as anti-Gram-positive agents, in particular to counter infections of methicillin-resistant strains. The chemical profiles showed differences between floristic regions but similarity within the same plant parts.
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http://dx.doi.org/10.7717/peerj.6893DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6510216PMC
May 2019

Evaluation of six regions for their potential as DNA barcodes in epiphyllous liverworts from Thailand.

Appl Plant Sci 2018 Aug 20;6(8):e01174. Epub 2018 Aug 20.

Department of Botany Faculty of Science Kasetsart University Chatuchak Bangkok 10900, Thailand.

Premise Of The Study: Studies on the diversity of epiphyllous bryophytes have been limited because of minute and incomplete specimens and a lack of taxonomic expertise. The recent development of the DNA barcoding approach has allowed taxon identification and species discovery of many obscure groups of organisms.

Methods: With DNA extractions from 99 samples of 16 species, we compared the efficiencies of six DNA markers (, , , , ITS1, and ITS2) in their ability to amplify, using a standard set of primers, as well as their discriminatory power, using distance-based and tree-based approaches with nucleotide data.

Results: The amplification success was relatively high (70-90%) with all of the markers, except for , which yielded no success. The barcoding gap, as calculated from the difference between inter- and intraspecific genetic distances, was the highest in ITS2, whereas the highest numbers of monophyletic groups were found with ITS2 and .

Discussion: should be used as a main barcoding marker with the addition of ITS2 for epiphyllous species. The development of DNA barcoding as a tool for quantifying species diversity will provide a rapid and reliable identification tool for epiphyllous bryophytes.
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http://dx.doi.org/10.1002/aps3.1174DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6110246PMC
August 2018

On the diversity and richness of understory bryophytes at Nectandra Cloud Forest Reserve, Costa Rica.

Biodivers Data J 2017 24(5):e11778. Epub 2017 Mar 24.

Nectandra Institute, San Ramon, Alajuela, Costa Rica.

Background: A survey of the understory bryophytes in the Nectandra Cloud Forest Preserve yielded 1083 specimens distributed among 55 families, represented by 74 genera of mosses, 75 genera of liverworts and 3 of hornworts. We studied and analyzed the bryophytic distribution on six types of substrates: 1) corticolous, 2) epiphyllous, 3) saxicolous, 4) terricolous, 5) aquatic and 6) lignicolous. The richness and composition of bryophyte genera are compared to those of other previous bryophyte surveys from 4 other sites with different oceanic exposures, climatic and geographic conditions in Costa Rica.

New Information: This is a report of the first extensive general survey of bryophytes at the Nectandra Reserve, a premontane cloud forest located on the Atlantic slope of Costa Rica, an area much less studied compared to the Monteverde cloud forest on the Pacific slope.
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http://dx.doi.org/10.3897/BDJ.5.e11778DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5515068PMC
March 2017

A temporal banding approach for consistent taxonomic ranking above the species level.

Sci Rep 2017 05 23;7(1):2297. Epub 2017 May 23.

Science & Education, Field Museum of Natural History, 1400 S Lake Shore Drive, Chicago, IL, 60605, USA.

Comparable taxonomic ranks within clades can facilitate more consistent classifications and objective comparisons among taxa. Here we use a temporal approach to identify taxonomic ranks. This is an extension of the temporal banding approach including a Temporal Error Score that finds an objective cut-off for each taxonomic rank using information for the current classification. We illustrate this method using a data set of the lichenized fungal family Parmeliaceae. To assess its performance, we simulated the effect of taxon sampling and compared our method with the other temporal banding method. For our sampled phylogeny, 11 of the 12 included families remained intact and 55 genera were confirmed, whereas 32 genera were lumped and 15 genera were split. Taxon sampling impacted the method at the genus level, whereas yielded only insignificant changes at the family level. The other available temporal approach also gives a similar cutoff point to our method. Our approach to identify taxonomic ranks enables taxonomists to revise and propose classifications on an objective basis, changing ranks of clades only when inconsistent with most taxa in a phylogenetic tree. An R script to find the time point with the minimal temporal error is provided.
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http://dx.doi.org/10.1038/s41598-017-02477-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5442095PMC
May 2017

Cryptic diversity and symbiont interactions in rock-posy lichens.

Mol Phylogenet Evol 2016 06 24;99:261-274. Epub 2016 Mar 24.

Science & Education, The Field Museum, Chicago, IL, USA.

Identifying factors that influence species interactions is central to research in symbiotic systems. While lichens represent iconic models of symbiosis and play important roles in understanding the biology of symbiotic interactions, patterns of interactions in lichen symbionts and mechanisms governing these relationships are not well characterized. This is due, in part to the fact that current taxonomic approaches for recognizing diversity in lichen symbionts commonly fail to accurately reflect actual species diversity. In this study, we employed DNA-based approaches to circumscribed candidate species-level lineages in rock-posy lichen symbionts (mycobiont=Rhizoplaca s. lat. species; photobiont=Trebouxia species). Our results revealed a high degree of cryptic diversity in both the myco- and photobionts in these lichens. Using the candidate species circumscribed here, we investigated the specificity of the symbionts toward their partners and inferred the relative importance of various factors influencing symbiont interactions. Distinct mycobiont species complexes, ecozones, and biomes are significantly correlated with the occurrence of photobiont OTUs, indicating that complex interactions among mycobiont lineages, ecogeography, and microhabitat determine interactions between photobionts and their mycobionts in lichen symbiosis. One-to-one specificity between mycobiont and photobiont species was not found, with the exception of R. maheui that associated with a single Trebouxia OTU that was not found with other Rhizoplaca s. lat. species. We estimated the most recent common ancestor of the core Rhizoplaca group at c. 62.5Ma, similar in age to the diverse parmelioid core group in the well-studied family Parmeliaceae. However, in contrast to Parmeliaceae, species in Rhizoplaca were found to associate with a narrow range of photobionts. Our study provides important perspectives into species diversity and interactions in iconic lichen symbiotic systems and establishes a valuable framework for continuing research into rock-posy lichens.
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http://dx.doi.org/10.1016/j.ympev.2016.03.030DOI Listing
June 2016

Fungal specificity and selectivity for algae play a major role in determining lichen partnerships across diverse ecogeographic regions in the lichen-forming family Parmeliaceae (Ascomycota).

Mol Ecol 2015 07 14;24(14):3779-97. Epub 2015 Jul 14.

Science & Education, The Field Museum, Chicago, IL, USA.

Microbial symbionts are instrumental to the ecological and long-term evolutionary success of their hosts, and the central role of symbiotic interactions is increasingly recognized across the vast majority of life. Lichens provide an iconic group for investigating patterns in species interactions; however, relationships among lichen symbionts are often masked by uncertain species boundaries or an inability to reliably identify symbionts. The species-rich lichen-forming fungal family Parmeliaceae provides a diverse group for assessing patterns of interactions of algal symbionts, and our study addresses patterns of lichen symbiont interactions at the largest geographic and taxonomic scales attempted to date. We analysed a total of 2356 algal internal transcribed spacer (ITS) region sequences collected from lichens representing ten mycobiont genera in Parmeliaceae, two genera in Lecanoraceae and 26 cultured Trebouxia strains. Algal ITS sequences were grouped into operational taxonomic units (OTUs); we attempted to validate the evolutionary independence of a subset of the inferred OTUs using chloroplast and mitochondrial loci. We explored the patterns of symbiont interactions in these lichens based on ecogeographic distributions and mycobiont taxonomy. We found high levels of undescribed diversity in Trebouxia, broad distributions across distinct ecoregions for many photobiont OTUs and varying levels of mycobiont selectivity and specificity towards the photobiont. Based on these results, we conclude that fungal specificity and selectivity for algal partners play a major role in determining lichen partnerships, potentially superseding ecology, at least at the ecogeographic scale investigated here. To facilitate effective communication and consistency across future studies, we propose a provisional naming system for Trebouxia photobionts and provide representative sequences for each OTU circumscribed in this study.
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http://dx.doi.org/10.1111/mec.13271DOI Listing
July 2015

A Tale of Two Hyper-diversities: Diversification dynamics of the two largest families of lichenized fungi.

Sci Rep 2015 May 6;5:10028. Epub 2015 May 6.

Science and Education, The Field Museum, 1400 S Lake Shore Drive, Chicago, IL 60605 USA.

Renewed interests in macroevolutionary dynamics have led to the proliferation of studies on diversification processes in large taxonomic groups, such as angiosperms, mammals, and birds. However, such a study has yet to be conducted in lichenized fungi--an extremely successful and diverse group of fungi. Analysing the most comprehensive time-calibrated phylogenies with a new analytical method, we illustrated drastically different diversification dynamics between two hyper-diverse families of lichenized fungi, Graphidaceae and Parmeliaceae, which represent more than a fourth of the total species diversity of lichenized fungi. Despite adopting a similar nutrition mode and having a similar number of species, Graphidaceae exhibited a lower speciation rate, while Parmeliaceae showed a sharp increase in speciation rate that corresponded with the aridification during the Oligocene-Miocene transition, suggesting their adaptive radiation into a novel arid habitat.
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http://dx.doi.org/10.1038/srep10028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4421861PMC
May 2015

Characterization of fungus-specific microsatellite markers in the lichen-forming fungus Parmelina carporrhizans (Parmeliaceae).

Appl Plant Sci 2014 Dec 20;2(12). Epub 2014 Nov 20.

Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Plaza de Ramón y Cajal s/n, Madrid 28040, Spain.

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Premise Of The Study: Microsatellite loci were developed to study the lichen-forming fungus Parmelina (Parmeliaceae) in different habitats of western Europe and the Mediterranean for baseline studies to understand the effects of climate change on its distribution. •

Methods And Results: We cultured P. carporrhizans from ascospores for genomic sequencing with Illumina HiSeq. We successfully developed 11 polymorphic microsatellite markers and associated primer sets and assessed them with 30 individuals from two of the Canary Islands. The average number of alleles per locus was 8.8. Nei's unbiased gene diversity of these loci ranged from 0.53 to 0.91 in the tested populations. Amplification in two closely related species (P. tiliacea, P. cryptotiliacea) yielded only limited success. •

Conclusions: The new microsatellite markers will allow the study of genetic diversity and population structure in P. carporrhizans. We propose eight markers to combine in two multiplex reactions for further studies on a larger set of populations.
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http://dx.doi.org/10.3732/apps.1400081DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4259457PMC
December 2014

Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi.

Database (Oxford) 2014 30;2014. Epub 2014 Jun 30.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA, CBS-KNAW Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The Netherlands, Department of Pharmaceutical Sciences - Microbiology, Università degli Studi di Perugia, Perugia, Italy, Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney Medical School-Westmead Hospital, The University of Sydney, Westmead Millennium Institute, Westmead, Australia, Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Göteborg, Sweden, Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN 37920, USA, Illinois Natural History Survey, University of Illinois, 1816 South Oak Street, Champaign, IL 61820, USA, Mycology Section, Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS, UK, Natural History Museum, University of Tartu, 46 Vanemuise, 51014 Tartu, Estonia, Purdue University, Department of Botany and Plant Pathology, 915 W. State Street, West Lafayette, IN 47907, USA, Institute of Excellence in Fungal Research, and School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand, Imperial College London, Royal Botanic Gardens, Kew TW9 3DS, England, UK, Muséum National d'Histoire Naturelle, Dépt. Systématique et Evolution CP39, UMR7205, 12 Rue Buffon, F-75005 Paris, France, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, P. R. China, Departamento de Biología Vegetal II, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid 28040, Spain, Senckenberg Museum of Natural History Görlitz, PF 300 154, 02806 Görlitz, Germany, Department of Microbiology and Plant Pathology, Forestry Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0001, South Africa, Real Jardín Botánico, RJB-CSIC,

DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi. Database URL: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA177353.
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http://dx.doi.org/10.1093/database/bau061DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4075928PMC
February 2015

Asexual propagules as an adaptive trait for epiphylly in tropical leafy liverworts (Lejeuneaceae).

Authors:
Ekaphan Kraichak

Am J Bot 2012 Sep 21;99(9):1436-44. Epub 2012 Aug 21.

Department of Integrative Biology, 4156 Valley Life Sciences Building #3140, University of California, Berkeley, California 94720, USA.

Premise Of The Study: Many links between form and function are described in the context of adaptation. Several morphological and life-history traits in the leafy liverwort family Lejeuneaceae (Marchantiophyta) have been hypothesized to be adaptations for living on the surface of leaves of vascular plants (epiphylly). There have been, however, no rigorous tests of these hypotheses.

Methods: Using a recently published phylogeny of Lejeuneaceae and trait data from published monographs, I tested the correlations of putative adaptive traits with the incidence of epiphylly. Both cross-species and phylogenetic-based analyses of trait data were performed to distinguish the patterns of shared evolutionary history from independent origins of putatively adaptive traits. The rates of transitions between different combinations of character states were also calculated to determine whether traits were more likely to evolve in the presence of epiphylly.

Key Results: Only one trait, production of asexual propagules, was correlated with epiphylly in the phylogenetic-based analysis. The rate of transition to asexual propagules was also significantly higher in the presence of epiphylly. Other traits correlated with epiphylly appeared to be the results of shared evolutionary history among sister taxa and therefore not due to adaptive evolution.

Conclusion: The present study distinguished production of asexual propagules from other traits as a key adaptive response to living on the leaf surface. No other putative "adaptive" traits to epiphylly showed evidence of being specific adaptation to epiphylly. The results highlight the importance of phylogenetically controlled methods in determining an adaptive function of traits.
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http://dx.doi.org/10.3732/ajb.1200120DOI Listing
September 2012
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