Ekaphan Kraichak
Kasetsart University, Sciences,Faculty of Botany, Faculty Member
- Currently a lecturer in Botany at Kasetsart University, Thailand, where I teach and study ecology and evolution of br... moreCurrently a lecturer in Botany at Kasetsart University, Thailand, where I teach and study ecology and evolution of bryophytes and lichens.
A recent Ph.D. from the department of Integrative biology at University of California, Berkeley. My dissertation research focused on understanding adaptation and community assembly of a unique group of bryophytes that live primarily on the leaf surface (epiphyllous bryophytes).edit
Hybrids between the critically endangered Siamese crocodile (Crocodylus siamensis) and least-concern saltwater crocodile (C. porosus) in captive populations represent a serious challenge for conservation and reintroduction programs due to... more
Hybrids between the critically endangered Siamese crocodile (Crocodylus siamensis) and least-concern saltwater crocodile (C. porosus) in captive populations represent a serious challenge for conservation and reintroduction programs due to the impact of anthropogenic activities. A previous study used microsatellite and mitochondrial DNA data to establish the criteria for identifying species and their hybrids; however, the results may have been influenced by biased allelic frequencies and genetic drift within the examined population. To overcome these limitations and identify the true signals of selection, alternative DNA markers and a diverse set of populations should be employed. Therefore, this study used DArT sequencing to identify genome-wide single nucleotide polymorphisms (SNPs) in both species and confirm the genetic scenario of the parental species and their hybrids. A population of saltwater crocodiles from Australia was used to compare the distribution of species-diagnostic...
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Abstract Jade perch (Scortum barcoo) is a new teleost in the developing aquaculture freshwater finfish grow-out sector in Australia and China. However, key information on the breeding sex determination system (SDS) remains poorly... more
Abstract Jade perch (Scortum barcoo) is a new teleost in the developing aquaculture freshwater finfish grow-out sector in Australia and China. However, key information on the breeding sex determination system (SDS) remains poorly understood, hampering sex control programs and genetic improvement. In this study, the jade perch SDS was examined by investigating genome-wide single-nucleotide polymorphisms (SNPs) using diversity arrays technology and cytogenetics analysis to identify the genomic variants associated with sex-linked regions. Although the cytogenetic results showed no variation in the chromosomal patterns between males and females, one male-specific locus and 13 male-linked loci were observed, suggesting that jade perch exhibits male heterogametic XX/XY SDS. Male-specific loci on the putative Y sex chromosome were also identified as an extremely small proportion of the genome. A homology search of the SNP loci revealed the male-specific loci were homologous to the Gypsy transposable element. This might be a remnant of an initial accumulation of repeats on the Y chromosome at the early stage of sex chromosome differentiation. The results provide a base for sex control breeding biotechnologies and genetic improvements to promote sexual size dimorphism and other new approaches to improve the commercial value of jade perch.
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DNA barcoding without assessing reliability and validity causes taxonomic errors of species identification, which is responsible for disruptions of their conservation and aquaculture industry. Although DNA barcoding facilitates molecular... more
DNA barcoding without assessing reliability and validity causes taxonomic errors of species identification, which is responsible for disruptions of their conservation and aquaculture industry. Although DNA barcoding facilitates molecular identification and phylogenetic analysis of species, its availability in clariid catfish lineage remains uncertain. In this study, DNA barcoding was developed and validated for clariid catfish. 2,970 barcode sequences from mitochondrial cytochrome c oxidase I (COI) and cytochrome b (Cytb) genes and D-loop sequences were analyzed for 37 clariid catfish species. The highest intraspecific nearest neighbor distances were 85.47%, 98.03%, and 89.10% for COI, Cytb, and D-loop sequences, respectively. This suggests that the Cytb gene is the most appropriate for identifying clariid catfish and can serve as a standard region for DNA barcoding. A positive barcoding gap between interspecific and intraspecific sequence divergence was observed in the Cytb dataset...
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Microsatellites are polymorphic and cost-effective. Optimizing reduced microsatellite panels using heuristic algorithms eases budget constraints in genetic diversity and population genetic assessments. Microsatellite marker efficiency is... more
Microsatellites are polymorphic and cost-effective. Optimizing reduced microsatellite panels using heuristic algorithms eases budget constraints in genetic diversity and population genetic assessments. Microsatellite marker efficiency is strongly associated with its polymorphism and is quantified as the polymorphic information content (PIC). Nevertheless, marker selection cannot rely solely on PIC. In this study, the ant colony optimization (ACO) algorithm, a widely recognized optimization method, was adopted to create an enhanced selection scheme for refining microsatellite marker panels, called the PIC–ACO selection scheme. The algorithm was fine-tuned and validated using extensive datasets of chicken (Gallus gallus) and Chinese gorals (Naemorhedus griseus) from our previous studies. In contrast to basic optimization algorithms that stochastically initialize potential outputs, our selection algorithm utilizes the PIC values of markers to prime the ACO process. This increases the g...
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Cassava breeding is a critical aspect of sustainable agriculture to address the challenges of food security and climate change. The present study aimed to assess the combining ability of six Thai cassava elite varieties for four key... more
Cassava breeding is a critical aspect of sustainable agriculture to address the challenges of food security and climate change. The present study aimed to assess the combining ability of six Thai cassava elite varieties for four key traits, including fresh root yield (FRY), fresh shoot yield (FSY), harvest index (HI) and starch content (SC) through an analysis of the diallel mating design over two years. Parental lines HB80 and R5 showed significant positive general combining ability (GCA) effects for high SC; R1 and HB80 for low FSY; and R1 for high FRY and HI. The genetic effects for FSY, SC and HI were primarily influenced by the GCA of the progenitors, while specific combining ability (SCA) was more important for the FRY than the other three traits. Cultivation conditions were also found to impact the evaluation of genetic effects, with a poor growing environment affecting the expression of the genotype. This study provides a useful basis for the selection of parental lines for ...
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Leucobryum scalare was described in 1904 but its taxonomic status has been disputed, being reduced to a variety of Leucobryum aduncum or synonymized with Leucobryum aduncum. The taxonomic confusion of this taxon has remained unresolved.... more
Leucobryum scalare was described in 1904 but its taxonomic status has been disputed, being reduced to a variety of Leucobryum aduncum or synonymized with Leucobryum aduncum. The taxonomic confusion of this taxon has remained unresolved. Hence, we revisited the taxonomic status of the taxon using phylogenetic and morphometric approaches. A total of 27 samples from Leucobryum aduncum var. aduncum and Leucobryum aduncum var. scalare were used to generate data from four markers, including ITS1, ITS2, atpB-rbcL spacer, and trnL-trnF. The concatenated dataset was used to reconstruct a phylogenetic tree. Both qualitative and quantitative morphological characters were measured and analyzed with Principal Component Analysis (PCA) and PERMANOVA. The results showed that the two taxa are closely related but they are reciprocally monophyletic. Both qualitative and quantitative characters could also separate Leucobryum aduncum var. scalare from Leucobryum aduncum var. aduncum as shown with PCA an...
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The African catfish (Clarias gariepinus) may exhibit the co-existence of XX/XY and ZZ/ZW sex-determination systems (SDSs). However, the SDS of African catfish might be influenced by a polygenic sex-determination (PSD) system, comprising... more
The African catfish (Clarias gariepinus) may exhibit the co-existence of XX/XY and ZZ/ZW sex-determination systems (SDSs). However, the SDS of African catfish might be influenced by a polygenic sex-determination (PSD) system, comprising multiple independently segregating sex “switch” loci to determine sex within a species. Here, we aimed to detect the existence of PSD using hybrid. The hybrid produced by crossing male African catfish with female bighead catfish (C. macrocephalus, XX/XY) is a good animal model to study SDSs. Determining the SDS of hybrid catfish can help in understanding the interactions between these two complex SDS systems. Using the genotyping-by-sequencing “DART-seq” approach, we detected seven moderately male-linked loci and seventeen female-linked loci across all the examined hybrid specimens. Most of these loci were not sex-linked in the parental species, suggesting that the hybrid exhibits a combination of different alleles. Annotation of the identified sex-l...
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Aneuraceae is the largest family of the simple thalloid liverworts. Despite simple morphological features, this family is well-known for its unique ecology, cryptic diversity, and species-rich lineages. In this study, we explored the... more
Aneuraceae is the largest family of the simple thalloid liverworts. Despite simple morphological features, this family is well-known for its unique ecology, cryptic diversity, and species-rich lineages. In this study, we explored the evolutionary history and diversification of the Aneuraceae. Investigating the effects of fossil calibrations on divergence time estimates and how recognizing cryptic species impacts macroevolutionary analyses. We used publicly available nucleotide sequences to reconstruct chronograms of Aneuraceae with representatives from subclass Metzgeriidae as outgroups. We also examined the consequences of different calibrations in chronogram reconstruction. Then, the resulting time-calibrated phylogeny was employed to reveal diversification dynamics with lineage through time plots (LTTPs), γ-statistics, and Bayesian Analysis of Macroevolutionary Mixtures (BAMM). The Aneuraceae had originated and created diversity since the Lower Carboniferous (352.75 Mya, 95%HPD: ...
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Fire is a necessary disturbance in tropical deciduous forests, as it helps clear the understory community and allows regeneration of grasses and forbs for local wildlife. Huai Kha Khaeng Wildlife Sanctuary (HKK) and Huai Thab Salao-Huai... more
Fire is a necessary disturbance in tropical deciduous forests, as it helps clear the understory community and allows regeneration of grasses and forbs for local wildlife. Huai Kha Khaeng Wildlife Sanctuary (HKK) and Huai Thab Salao-Huai Rabum Non-Hunting Area (HTS) are parts of a few places in Southeast Asia with deciduous forests. However, this area was heavily logged up until 1989, followed by a long period of fire suppression. The consequences of these changes on understory communities have not been investigated. Therefore, the current study aimed to examine the understory communities and their aboveground biomass before and after the annual prescribed burns in HKK and HTS. Understory plant composition and biomass were surveyed in November 2018 (before the fire) and May 2019 (three months after the fire) in 128 temporary plots, covering of deciduous dipterocarp forest, mixed deciduous forest, mixed deciduous forest with bamboo, and open area. We identified a total of 480 understo...
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Forage plants, as primary producers, play an essential role in maintaining populations of large herbivores. The availability and quality of these forage plants can affect the health and viability of these animals. Seasonally dry forests... more
Forage plants, as primary producers, play an essential role in maintaining populations of large herbivores. The availability and quality of these forage plants can affect the health and viability of these animals. Seasonally dry forests of Huai Kha Khaeng Wildlife Sanctuary and Huai Thab Salao-Huai Rabum Non-Hunting Area are recognized as one of the largest contiguous pieces of forests in mainland Southeast Asia and serve as a home to many large herbivore species, particularly banteng (Bos javanicus birmanicus). However, our understanding of forage plants and their dynamics is still limited. Therefore, the current study was undertaken to understand the dynamics of forage plants, prescribed burning effects, and the associated environmental factors. During 2018–2019, the results showed that the highest forage availability was in June after the prescribed burns at 156.2–252.6 kg ha−1 and the lowest in February before the burning at 16.8–39.8 kg ha−1. Environmental factors that impacted...
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Centromeric satellite DNA (cen-satDNA) consists of highly divergent repeat monomers, each approximately 171 base pairs in length. Here, we investigated the genetic diversity in the centromeric region of two primate species: long-tailed... more
Centromeric satellite DNA (cen-satDNA) consists of highly divergent repeat monomers, each approximately 171 base pairs in length. Here, we investigated the genetic diversity in the centromeric region of two primate species: long-tailed (Macaca fascicularis) and rhesus (Macaca mulatta) macaques. Fluorescence in situ hybridization and bioinformatic analysis showed the chromosome-specific organization and dynamic nature of cen-satDNAsequences, and their substantial diversity, with distinct subfamilies across macaque populations, suggesting increased turnovers. Comparative genomics identified high level polymorphisms spanning a 120 bp deletion region and a remarkable interspecific variability in cen-satDNA size and structure. Population structure analysis detected admixture patterns within populations, indicating their high divergence and rapid evolution. However, differences in cen-satDNA profiles appear to not be involved in hybrid incompatibility between the two species. Our study pr...
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Fishes provide a unique and intriguing model system for studying the genomic origin and evolutionary mechanisms underlying sex determination and high sex-chromosome turnover. In this study, the mode of sex determination was investigated... more
Fishes provide a unique and intriguing model system for studying the genomic origin and evolutionary mechanisms underlying sex determination and high sex-chromosome turnover. In this study, the mode of sex determination was investigated in Siamese fighting fish, a species of commercial importance. Genome-wide SNP analyses were performed on 75 individuals (40 males and 35 females) across commercial populations to determine candidate sex-specific/sex-linked loci. In total, 73 male-specific loci were identified and mapped to a 5.6 kb region on chromosome 9, suggesting a putative male-determining region (pMDR) containing localized dmrt1 and znrf3 functional sex developmental genes. Repeat annotations of the pMDR revealed an abundance of transposable elements, particularly Ty3/Gypsy and novel repeats. Remarkably, two out of the 73 male-specific loci were located on chromosomes 7 and 19, implying the existence of polygenic sex determination. Besides male-specific loci, five female-specifi...
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Sex-specific loci are powerful tools for identifying sex determination systems. They offer a molecular biotechnological approach for producing all‐male or all-female fish for commercial breeding. The North African catfish has been widely... more
Sex-specific loci are powerful tools for identifying sex determination systems. They offer a molecular biotechnological approach for producing all‐male or all-female fish for commercial breeding. The North African catfish 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. North African catfish have either a ZZ/ZW or XX/XY sex determination system. Here, we investigate and characterize these systems using high-throughput genome complexity reduction sequencing. This approach was effective for identifying sex-specific loci with both single-nucleotide polymorphisms (SNPs) and restriction fragment presence/absence (PA) markers in 30 phenotypic sex assignments of North African catfish. In total, 41 male-linked loci met the criteria of moderately sex-linked loci (70:30, male:female; 80:20, male:female). By contrast, only 25 female-...
Most lizards in the Superfamily Iguanoidea have an XX/XY sex determination system in which sex chromosomal linkage has homology with chicken (Gallus gallus) chromosome 15 (GGA15); however, sex chromosome genomics remains largely... more
Most lizards in the Superfamily Iguanoidea have an XX/XY sex determination system in which sex chromosomal linkage has homology with chicken (Gallus gallus) chromosome 15 (GGA15); however, sex chromosome genomics remains largely unexplored due to the presence of homomorphic sex chromosomes in many species. Recent advances in high-throughput sequencing with genome complexity reduction now provide an effective approach to identify sex-specific loci in both single nucleotide polymorphisms (SNPs) and restriction fragment presence/absence (PA), and a better understanding of sex chromosome dynamics in this lineage. Here, we applied Diversity Arrays Technology (DArTseq™) in 29 phenotypic sex assignments of green iguana (Iguana 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, likely serving as evidence indicative of XY recombination. 3 loci from perfectly sex-...
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... more
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
Concatenated ITS, COXII, rbcL, and psbJ matrix for representatives of the T. arboricola/gigantea grou
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Alignment of all Trebouxia ITS sequences belonging to the T. impressa/gelatinosa clad
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Alignment of all Trebouxia ITS sequences belonging to the T. galapagensis/usneae clad
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Alignment of all Trebouxia ITS sequences belonging to the T. arboricola/gigantea clad
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Complete Trebouxia ITS alignment (n=2356), clades 'A', 'G', 'I', and 'S'
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Supplementary Table S2. Summary of the taxonomic and geographic sampling of fungal genera for this study. Supplementary Table S3. Specificity indices for Trebouxia OTUs represented by ≥ 10 sequences per OTU, based on fungal genera... more
Supplementary Table S2. Summary of the taxonomic and geographic sampling of fungal genera for this study. Supplementary Table S3. Specificity indices for Trebouxia OTUs represented by ≥ 10 sequences per OTU, based on fungal genera included in this study. Supplementary Table S4. Summary of OTUs inferred using the ABGD detection program (Puillandre et al. 2012) represented by at least ten sequences and/or including sequences generated from UTEX and SAG cultures (UTEX and SAG cultures are shown in bold). Cultures and/or provisional names from previous studies, geographic distributions, and associated mycobiont hosts are reported. Other lichen mycobiont genera associated with Trebouxia OTUs were inferred using a BLAST search against the GenBank Nucleotide sequence database (searched 15 Nov 2014), where sequences with ≥ 98% similarity to a representative sequence from each OTU were assumed to belong to the OTU. The majority of OTUs were largely consistent with 97.5% sequence similarity clusters, with the exception of OTU ‘I01’, which was split into ten OTUs at 97.5%. The 97.5% sequence similarity clusters for OTUs ‘I01’ are shown parenthetically for each mycobiont host. Supplementary Figure S1. Relative proportion of Trebouxia OTUs associated with sampled fungal genera Supplementary Figure S2. ITS gene tree for a subset of specimens in the T. arboricola/gigantea group inferred using the program RAxML. Supplementary Figure S3. Mitochondrial COXII gene tree for a subset of specimens in the T. arboricola/gigantea group inferred using the program RAxML. Supplementary Figure S4. Chloroplast rbcL gene tree for a subset of specimens in the T. arboricola/gigantea group inferred using the program RAxML. Supplementary Figure S5. Chloroplast psbJ-L gene tree for a subset of specimens in the T. arboricola/gigantea group inferred using the program RAxML. Ambiguous regions of the alignment were removed using the program Gblocks. Supplementary Figure S6. Chloroplast topology for a subset of specimens in the T. arboricola/gigantea group inferred from concatenated rbcL and psJ-L alignments using the program RAxML. Supplementary Figure S7. A “total evidence” phylogeny for the T. arboricola/gigantea, inferred from concatenated nuclear ITS, mitochondrial COXII, and the chloroplast markers rbcL and psbJ-L using the program RAxML
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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... more
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