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Article ; Online: Gene conservation of six Hungarian local chicken breeds maintained in small populations over time

Nora Palinkas-Bodzsar / Nikoletta Sztan / Tamas Molnar / Andras Hidas / Tzen-Yuh Chiang

PLoS ONE, Vol 15, Iss

2020 Volume 9

Abstract: Investigation into the genetic diversity of certain endangered native breeds of domestic animals has been in common practice for several decades. The primary objective of these investigations has been to reveal the exceptional genetic value of such ... ...

Abstract	Investigation into the genetic diversity of certain endangered native breeds of domestic animals has been in common practice for several decades. The primary objective of these investigations has been to reveal the exceptional genetic value of such breeds, both for their conservation and also to gain insight into their current genetic status, as they have been undergoing a progressive decrease in population size and general diversity; this has been compounded by the general lack of an optimal breeding scheme. In this study, we have investigated changes in the genetic diversity of six Hungarian local chicken breeds based on 29 microsatellite loci over a period of 15 years. In terms of the basic diversity measures, populations sampled in 2017 generally exhibited a lower heterozygosity and mean number of alleles and thus, experienced a higher degree of inbreeding. Although the effective population size increased, the estimates of populations sampled over different periods indicated comparatively low values, suggesting overall lower genetic variance. Pairwise FST estimates were higher in the populations sampled in 2017, showing a larger genetic distance between them. Considerable differences exist between the populations of the same breeds, which can most likely be attributed to genetic drift. STRUCTURE results have shown a clear separation between the Hungarian populations, which is in agreement with the principal coordinate analysis. The most likely clustering was found at K = 6, classifying the populations of the same breed as one group. No considerable allele loss was found in the Hungarian indigenous chicken breeds after 15 years of conservation. In general terms, after 15 years, the level of inbreeding within the populations was, in fact, higher, although this could be effectively reduced through the use of an improved mating system. Consequently, the breed management applied in the case of Hungarian local chicken breeds was found to be effective at adequately conserving their genetic variability.
Keywords	Medicine ; R ; Science ; Q
Subject code	630
Language	English
Publishing date	2020-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Highly diverse endophytes in roots of Cycas bifida (Cycadaceae), an ancient but endangered gymnosperm

Zheng, Ying / Tzen-Yuh Chiang / Chao-Li Huang / Xun Gong

journal of microbiology. 2018 May, v. 56, no. 5

2018

Abstract: As an ancient seed plant, cycads are one of the few gymnosperms that develop a root symbiosis with cyanobacteria, which has allowed cycads to cope with harsh geologic and climatic conditions during the evolutionary process. However, the endophytic ... ...

Abstract	As an ancient seed plant, cycads are one of the few gymnosperms that develop a root symbiosis with cyanobacteria, which has allowed cycads to cope with harsh geologic and climatic conditions during the evolutionary process. However, the endophytic microbes in cycad roots remain poorly identified. In this study, using next-generation sequencing techniques, we investigated the microbial diversity and composition of both the coralloid and regular roots of Cycas bifida (Dyer) K.D. Hill. Highly diverse endophytic communities were observed in both the coralloid and regular roots. Of the associated bacteria, the top five families were the Nostocaceae, Sinobacteraceae, Bradyrhizobiaceae, Bacillaceae, and Hyphomicrobiaceae. The Nectriaceae, Trichocomaceae, and Incertae sedis were the predominant fungal families in all root samples. A significant difference in the endophytic bacterial community was detected between coralloid roots and regular roots, but no difference was observed between the fungal communities in the two root types. Cyanobacteria were more dominant in coralloid roots than in regular roots. The divergence of cycad root structures and the modified physiological processes may have contributed to the abundance of cyanobionts in coralloid roots. Consequently, the colonization of cyanobacteria inhibits the assemblage of other endophytes. Our results contribute to an understanding of the species diversity and composition of the cycad-endophyte microbiome and provide an abbreviated list of potential ecological roles of the core microbes present.
Keywords	Bacillaceae ; Bradyrhizobiaceae ; Cycas ; Hyphomicrobiaceae ; Nectriaceae ; Nostocaceae ; Trichocomaceae ; bacteria ; bacterial communities ; climatic factors ; endophytes ; fungal communities ; fungi ; high-throughput nucleotide sequencing ; microbiome ; roots ; species diversity ; symbiosis
Language	English
Dates of publication	2018-05
Size	p. 337-345.
Publishing place	The Microbiological Society of Korea
Document type	Article
ZDB-ID	2012399-1
ISSN	1225-8873
ISSN	1225-8873
DOI	10.1007/s12275-018-7438-3
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Phylogeographic structure of the dunes sagebrush lizard, an endemic habitat specialist

Lauren M. Chan / Charles W. Painter / Michael T. Hill / Toby J. Hibbitts / Daniel J. Leavitt / Wade A. Ryberg / Danielle Walkup / Lee A. Fitzgerald / Tzen-Yuh Chiang

PLoS ONE, Vol 15, Iss

2020 Volume 9

Abstract: Phylogeographic divergence and population genetic diversity within species reflect the impacts of habitat connectivity, demographics, and landscape level processes in both the recent and distant past. Characterizing patterns of differentiation across the ...

Abstract	Phylogeographic divergence and population genetic diversity within species reflect the impacts of habitat connectivity, demographics, and landscape level processes in both the recent and distant past. Characterizing patterns of differentiation across the geographic range of a species provides insight on the roles of organismal and environmental traits in evolutionary divergence and future population persistence. This is particularly true of habitat specialists where habitat availability and resource dependence may result in pronounced genetic structure as well as increased population vulnerability. We use DNA sequence data as well as microsatellite genotypes to estimate range-wide phylogeographic divergence, historical population connectivity, and historical demographics in an endemic habitat specialist, the dunes sagebrush lizard (Sceloporus arenicolus). This species is found exclusively in dune blowouts and patches of open sand within the shinnery oak-sand dune ecosystem of southeastern New Mexico and adjacent Texas. We find evidence of phylogeographic structure consistent with breaks and constrictions in suitable habitat at the range-wide scale. In addition, we find support for a dynamic and variable evolutionary history across the range of S. arenicolus. Populations in the Monahans Sandhills have deeply divergent lineages consistent with long-term demographic stability. In contrast, populations in the Mescalero Sands are not highly differentiated, though we do find evidence of demographic expansion in some regions and relative demographic stability in others. Phylogeographic history and population genetic differentiation in this species has been shaped by the configuration of habitat patches within a geologically complex and historically dynamic landscape. Our findings identify regions as genetically distinctive conservation units as well as underscore the genetic and demographic history of different lineages of S. arenicolus.
Keywords	Medicine ; R ; Science ; Q
Subject code	333 ; 590
Language	English
Publishing date	2020-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Phylogeny of the Hylocomiaceae (Mosses, Order Hypnales) Inferred from Ontogenetic and Morphological Characteristics

Tzen-Yuh Chiang

Taiwania, Vol 45, Iss 1, Pp 66-

2000 Volume 94

Abstract: The phylogeny of Hylocomiaceae is inferred by cladistic analyses of twenty-nine morphological characters and the ontogenetic sequences of paraphyllia, central strands, and axillary hairs. The entire ontogenetic transformations are recognized as ... ...

Abstract	The phylogeny of Hylocomiaceae is inferred by cladistic analyses of twenty-nine morphological characters and the ontogenetic sequences of paraphyllia, central strands, and axillary hairs. The entire ontogenetic transformations are recognized as characters, and character variation is polarized by outgroup comparisons. Two equally parsimonious trees produced by heuristic searches of PAUP support the monophyly of the Hylocomiaceae, which is closely related to family Hypnaceae, containing eight genera Hylocomium, Loeskeobryum, Leptocladiella, Hylocomiastrum, Neodolichomitra, Macrothamnium, Leptohymenium, and Orontobryum. Hylocomiaceae is diagnosable by sympodial growth-form, excepting Orontobryum. The genera Rhytidium, Rhytidiadelphus, Pleurozium, and Rhytidioposis are excluded from the Hylocomiaceae and comprise a monophyletic family, Rhytidiaceae. Based on the reconstructed phylogeny, homology is tested by Patterson's tests of similarity, conjunction, and congruence. In Hylocomiaceae erect leaves without plication and absent of foliose pseudoparaphyllia are found to be symplesiomorphies; at the infrafamilial level erect capsules with reduced peristomes are homologous (i.e., derived from a recent common ancestor). Homoplasies also provide useful insights into understanding the mechanisms of morphological evolution. A complementary methodology synthesizing adaptationist and structuralist perspectives is employed. Convergent evolution of paraphyllia in mosses is ascribed to environmental selection. The Bauplan of conducting tissue in mosses is attributed to functional constraints. Reversed evolution of central strands in Loeskeobryum is a manifestation of developmental constraints, which channel the variation of the ontogenetic pathway. Heterochrony by truncating (paedomorphosis) or extending (peramorphosis) the ontogenetic sequences is a common mode of morphological evolution in the Hylocomiaceae. The parallel evolution of axillary hairs by retention of juvenile morphology at the adult stage in Hylocomiastrum, ...
Keywords	Hylocomiaceae ; Character concept ; Cladistics ; Monophyly ; Ontogenetic transformations ; Phylogeny ; Biology (General) ; QH301-705.5
Subject code	590
Language	English
Publishing date	2000-03-01T00:00:00Z
Publisher	National Taiwan University
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Effects of GC bias in next-generation-sequencing data on de novo genome assembly.

Yen-Chun Chen / Tsunglin Liu / Chun-Hui Yu / Tzen-Yuh Chiang / Chi-Chuan Hwang

PLoS ONE, Vol 8, Iss 4, p e

2013 Volume 62856

Abstract: Next-generation-sequencing (NGS) has revolutionized the field of genome assembly because of its much higher data throughput and much lower cost compared with traditional Sanger sequencing. However, NGS poses new computational challenges to de novo genome ...

Abstract	Next-generation-sequencing (NGS) has revolutionized the field of genome assembly because of its much higher data throughput and much lower cost compared with traditional Sanger sequencing. However, NGS poses new computational challenges to de novo genome assembly. Among the challenges, GC bias in NGS data is known to aggravate genome assembly. However, it is not clear to what extent GC bias affects genome assembly in general. In this work, we conduct a systematic analysis on the effects of GC bias on genome assembly. Our analyses reveal that GC bias only lowers assembly completeness when the degree of GC bias is above a threshold. At a strong GC bias, the assembly fragmentation due to GC bias can be explained by the low coverage of reads in the GC-poor or GC-rich regions of a genome. This effect is observed for all the assemblers under study. Increasing the total amount of NGS data thus rescues the assembly fragmentation because of GC bias. However, the amount of data needed for a full rescue depends on the distribution of GC contents. Both low and high coverage depths due to GC bias lower the accuracy of assembly. These pieces of information provide guidance toward a better de novo genome assembly in the presence of GC bias.
Keywords	Medicine ; R ; Science ; Q
Subject code	670
Language	English
Publishing date	2013-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Research data: (with research data) Biogeography of the Phalaenopsis amabilis species complex inferred from nuclear and plastid DNAs

Tsai, Chi-Chu / Chang-Hung Chou / Hao-Ven Wang / Tzen-Yuh Chiang / Ya-Zhu Ko / Yu-Chung Chiang

BMC plant biology. 2015 Dec., v. 15, no. 1

2015

Abstract: BACKGROUND: Phalaenopsis is one of the important commercial orchids in the world. Members of the P. amabilis species complex represent invaluable germplasm for the breeding program. However, the phylogeny of the P. amabilis species complex is still ... ...

Abstract	BACKGROUND: Phalaenopsis is one of the important commercial orchids in the world. Members of the P. amabilis species complex represent invaluable germplasm for the breeding program. However, the phylogeny of the P. amabilis species complex is still uncertain. The Phalaenopsis amabilis species complex (Orchidaceae) consists of subspecies amabilis, moluccana, and rosenstromii of P. amabilis, as well as P. aphrodite ssp. aphrodite, P. ap. ssp. formosana, and P. sanderiana. The aims of this study were to reconstruct the phylogeny and biogeographcial patterns of the species complex using Neighbor Joining (NJ), Maxinum Parsimony (MP), Bayesian Evolutionary Analysis Sampling Trees (BEAST) and Reconstruct Ancestral State in Phylogenies (RASP) analyses based on sequences of internal transcribed spacers 1 and 2 from the nuclear ribosomal DNA and the trnH-psbA spacer from the plastid DNA. RESULTS: A pattern of vicariance, dispersal, and vicarianceâ+âdispersal among disjunctly distributed taxa was uncovered based on RASP analysis. Although two subspecies of P. aphrodite could not be differentiated from each other in dispersal state, they were distinct from P. amabilis and P. sanderiana. Within P. amabilis, three subspecies were separated phylogenetically, in agreement with the vicariance or vicarianceâ+âdispersal scenario, with geographic subdivision along Huxleyâs, Wallaceâs and Lydekkerâs Lines. Molecular dating revealed such subdivisions among taxa of P. amabilis complex dating back to the late Pleistocene. Population-dynamic analyses using a Bayesian skyline plot suggested that the species complex experienced an in situ range expansion and population concentration during the late Last Glacial Maximum (LGM). CONCLUSIONS: Taxa of the P. amabilis complex with disjunct distributions were differentiated due to vicariance or vicarianceâ+âdispersal, with events likely occurring in the late Pleistocene. Demographic growth associated with the climatic oscillations in the WÃ¼rm glacial period followed the species splits. Nevertheless, a subsequent population slowdown occurred in the late LGM due to extinction of regional populations. The reduction of suitable habitats resulted in geographic fragmenttation of the remaining taxa.
Keywords	biogeography ; breeding programs ; germplasm ; habitats ; internal transcribed spacers ; Phalaenopsis ; phylogeny ; plastid DNA ; ribosomal DNA ; transcription (genetics) ; trees
Language	English
Dates of publication	2015-12
Size	p. 202.
Publishing place	BioMed Central
Document type	Article ; Research data
ISSN	1471-2229
DOI	10.1186/s12870-015-0560-z
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Frequent gene flow blurred taxonomic boundaries of sections in Lilium L. (Liliaceae).

Xun Gong / Kuo-Hsiang Hung / Yu-Wei Ting / Tsai-Wen Hsu / Lenka Malikova / Huyen Trang Tran / Chao-Li Huang / Shih-Hui Liu / Tzen-Yuh Chiang

PLoS ONE, Vol 12, Iss 8, p e

2017 Volume 0183209

Abstract: Gene flow between species may last a long time in plants. Reticulation inevitably causes difficulties in phylogenetic reconstruction. In this study, we looked into the genetic divergence and phylogeny of 20 Lilium species based on multilocus analyses of ... ...

Abstract	Gene flow between species may last a long time in plants. Reticulation inevitably causes difficulties in phylogenetic reconstruction. In this study, we looked into the genetic divergence and phylogeny of 20 Lilium species based on multilocus analyses of 8 genes of chloroplast DNA (cpDNA), the internally transcribed nuclear ribosomal DNA (nrITS) spacer and 20 loci extracted from the expressed sequence tag (EST) libraries of L. longiflorum Thunb. and L. formosanum Wallace. The phylogeny based on the combined data of the maternally inherited cpDNA and nrITS was largely consistent with the taxonomy of Lilium sections. This phylogeny was deemed the hypothetical species tree and uncovered three groups, i.e., Cluster A consisting of 4 taxa from the sections Pseudolirium and Liriotypus, Cluster B consisting of the 4 taxa from the sections Leucolirion, Archelirion and Daurolirion, and Cluster C comprising 10 taxa mostly from the sections Martagon and Sinomartagon. In contrast, systematic inconsistency occurred across the EST loci, with up to 19 genes (95%) displaying tree topologies deviating from the hypothetical species tree. The phylogenetic incongruence was likely attributable to the frequent genetic exchanges between species/sections, as indicated by the high levels of genetic recombination and the IMa analyses with the EST loci. Nevertheless, multilocus analysis could provide complementary information among the loci on the species split and the extent of gene flow between the species. In conclusion, this study not only detected frequent gene flow among Lilium sections that resulted in phylogenetic incongruence but also reconstructed a hypothetical species tree that gave insights into the nature of the complex relationships among Lilium species.
Keywords	Medicine ; R ; Science ; Q
Subject code	590
Language	English
Publishing date	2017-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Rubus amphidasys Focke (Rosaceae)

Tsai-Wen Hsu / Tzen-Yuh Chiang / Ching-I Peng

Taiwania, Vol 52, Iss 1, Pp 113-

A Newly Recorded Plant in Taiwan

2007 Volume 116

Abstract: Rubus, comprising about 700 species in the world, is a large genus of the family Rosaceae. Thirty-five species and four additional varieties were recorded in the 2nd edition of Flora of Taiwan. In the course of our botanical inventory, Rubus amphidasys ... ...

Abstract	Rubus, comprising about 700 species in the world, is a large genus of the family Rosaceae. Thirty-five species and four additional varieties were recorded in the 2nd edition of Flora of Taiwan. In the course of our botanical inventory, Rubus amphidasys Focke, heretofore unknown in Taiwan, was collected from northern part of the island. Rubus amphidasys is easily distinguished from other congenors by having a mixture of densely bristly hairs and glandular hairs on branches and calyx. In addition, small prickles are rarely found on its stems. In this report we provide a description, line drawings, and colored photographs taken from the wild to aid in identification.
Keywords	New record ; Rosaceae ; Rubus ; Rubus amphidasys ; Taiwan ; Taxonomy ; Biology (General) ; QH301-705.5
Language	English
Publishing date	2007-03-01T00:00:00Z
Publisher	National Taiwan University
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Characterization of 42 Microsatellite Markers from Poison Ivy, Toxicodendron radicans (Anacardiaceae)

Tzen-Yuh Chiang / Yu-Chung Chiang / Tsai-Wen Hsu / Huei-Chuan Shih / Chia-Chi Kuo

International Journal of Molecular Sciences, Vol 14, Iss 10, Pp 20414-

2013 Volume 20426

Abstract: Poison ivy, Toxicodendron radicans, and poison oaks, T. diversilobum and T. pubescens, are perennial woody species of the Anacardiaceae and are poisonous, containing strong allergens named urushiols that cause allergic contact dermatitis. Poison ivy is a ...

Abstract	Poison ivy, Toxicodendron radicans, and poison oaks, T. diversilobum and T. pubescens, are perennial woody species of the Anacardiaceae and are poisonous, containing strong allergens named urushiols that cause allergic contact dermatitis. Poison ivy is a species distributed from North America to East Asia, while T. diversilobum and T. pubescens are distributed in western and eastern North America, respectively. Phylogreography and population structure of these species remain unclear. Here, we developed microsatellite markers, via constructing a magnetic enriched microsatellite library, from poison ivy. We designed 51 primer pairs, 42 of which successfully yielded products that were subsequently tested for polymorphism in poison oak, and three subspecies of poison ivy. Among the 42 loci, 38 are polymorphic, while 4 are monomorphic. The number of alleles and the expected heterozygosity ranged from 1 to 12 and from 0.10 to 0.87, respectively, in poison ivy, while varied from 2 to 8 and, from 0.26 to 0.83, respectively in poison oak. Genetic analysis revealed distinct differentiation between poison ivy and poison oak, whereas slight genetic differentiation was detected among three subspecies of poison ivy. These highly polymorphic microsatellite fingerprints enable biologists to explore the population genetics, phylogeography, and speciation in Toxicodendron.
Keywords	genetic diversity ; microsatellite markers ; poison ivy ; poison oak ; population structuring ; Toxicodendron ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	590
Language	English
Publishing date	2013-10-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Multilocus Analyses Reveal Postglacial Demographic Shrinkage of Juniperus morrisonicola (Cupressaceae), a Dominant Alpine Species in Taiwan.

Chi-Chun Huang / Tsai-Wen Hsu / Hao-Ven Wang / Zin-Huang Liu / Yi-Yen Chen / Chi-Te Chiu / Chao-Li Huang / Kuo-Hsiang Hung / Tzen-Yuh Chiang

PLoS ONE, Vol 11, Iss 8, p e

2016 Volume 0161713

Abstract: Postglacial climate changes alter geographical distributions and diversity of species. Such ongoing changes often force species to migrate along the latitude/altitude. Altitudinal gradients represent assemblage of environmental, especially climatic, ... ...

Abstract	Postglacial climate changes alter geographical distributions and diversity of species. Such ongoing changes often force species to migrate along the latitude/altitude. Altitudinal gradients represent assemblage of environmental, especially climatic, variable factors that influence the plant distributions. Global warming that triggered upward migrations has therefore impacted the alpine plants on an island. In this study, we examined the genetic structure of Juniperus morrisonicola, a dominant alpine species in Taiwan, and inferred historical, demographic dynamics based on multilocus analyses. Lower levels of genetic diversity in north indicated that populations at higher latitudes were vulnerable to climate change, possibly related to historical alpine glaciers. Neither organellar DNA nor nuclear genes displayed geographical subdivisions, indicating that populations were likely interconnected before migrating upward to isolated mountain peaks, providing low possibilities of seed/pollen dispersal across mountain ranges. Bayesian skyline plots suggested steady population growth of J. morrisonicola followed by recent demographic contraction. In contrast, most lower-elevation plants experienced recent demographic expansion as a result of global warming. The endemic alpine conifer may have experienced dramatic climate changes over the alternation of glacial and interglacial periods, as indicated by a trend showing decreasing genetic diversity with the altitudinal gradient, plus a fact of upward migration.
Keywords	Medicine ; R ; Science ; Q
Language	English
Publishing date	2016-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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