scholarly journals Large-scale phylogenomics reveals ancient introgression in Asian Hepatica and new insights into the origin of the insular endemic Hepatica maxima

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Seongjun Park ◽  
SeonJoo Park
Keyword(s):  
Endemic Species ◽  
Evolutionary History ◽  
Large Scale ◽  
Oceanic Islands ◽  
Network Analyses ◽  
Organellar Genomes ◽  
History Of ◽  
Insular Endemic ◽  
Insular Endemic Species ◽  
Hybridization And Introgression

Abstract Hepatica maxima is native to Ulleungdo, which is one of the oceanic islands in Korea, and it likely originated via anagenetic speciation from the Korean mainland species H. asiatica. However, the relationships among the Asian lineages remain unresolved. Phylogenomics based on plant genomes can provide new insights into the evolutionary history of plants. We first generated plastid, mitochondrial and transcriptome sequences of the insular endemic species H. maxima. Using the genomic data for H. maxima, we obtained a phylogenomic dataset consisting of 76 plastid, 37 mitochondrial and 413 nuclear genes from Asian Hepatica and two outgroups. Coalescent- and concatenation-based methods revealed cytonuclear and organellar discordance in the lineage. The presence of gynodioecy with cytoplasmic male sterility in Asian Hepatica suggests that the discordance is correlated with potential disruption of linkage disequilibrium between the organellar genomes. Species network analyses revealed a deep history of hybridization and introgression in Asian Hepatica. We discovered that ancient and recent introgression events occurred throughout the evolutionary history of the insular endemic species H. maxima. The introgression may serve as an important source of genetic variation to facilitate adaptation to the Ulleungdo environment.

A new insular, endemic frog of the genus Kalophrynus Tschudi, 1838 (Anura: Microhylidae) from Tioman Island, Pahang, Peninsular MalaysiaDepartment of Biology, La Sierra University, 4500 Riverwalk Parkway, Riverside, California, 92515-8247 USA.

Zootaxa ◽  
2011 ◽  
Vol 3123 (1) ◽  
pp. 60
Author(s):  
CHAN KIN ONN ◽  
L. LEE GRISMER ◽  
JESSE GRISMER
Keyword(s):  
Endemic Species ◽  
Peninsular Malaysia ◽  
Southeastern Coast ◽  
Insular Endemic ◽  
Insular Endemic Species

A new insular, endemic species of microhylid frog of the genus Kalophrynus is described from Tioman Island, off the southeastern coast of Pahang, Peninsular Malaysia. Kalophrynus tiomanensis sp nov. can be differentiated from its congeners by the following combination of characters: SVL 21.4–26.3 mm; reduced webbing on toes; outer metatarsal tubercle absent; large, black inguinal spot and unique markings on dorsum. This discovery increases the number of endemic species of amphibians on Tioman Island to at least three.

scholarly journals RIP mutated ITS genes in populations of Ophiocordyceps sinensis and their implications for molecular systematics

IMA Fungus ◽  
2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Yi Li ◽  
Lan Jiang ◽  
Ke Wang ◽  
Hai-Jun Wu ◽  
Rui-Heng Yang ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Large Scale ◽  
Its Region ◽  
Wide Distribution ◽  
Specific Primers ◽  
Ophiocordyceps Sinensis ◽  
Single Genome ◽  
History Of ◽  
Geographic Populations ◽  
Internal Transcribed Spacer Sequences

Abstract Different hypotheses have been proposed to interpret the observed unusual ITS (internal transcribed spacer) sequences in Ophiocordyceps sinensis. The coexistence of diverged ITS paralogs in a single genome was previously shown by amplifying the ITS region from mono-ascospore isolates using specific primers designed for different ITS paralog groups. Among those paralogs, are AT-biased ITS sequences which were hypothesized to result from repeat-induced point mutation (RIP). This is a process that detects and mutates repetitive DNA and frequently leads to epigenetic silencing, and these mutations have been interpreted as pseudogenes. Here we investigate the occurrence and frequency of ITS pseudogenes in populations of O. sinensis using large-scale sampling, and discusses the implications of ITS pseudogenes for fungal phylogenetic and evolutionary studies. Our results demonstrate a wide distribution of ITS pseudogenes amongst different geographic populations, and indicate how ITS pseudogenes can contribute to the reconstruction of the evolutionary history of the species.

scholarly journals Shedding new light on opsin evolution

2011 ◽  
Vol 279 (1726) ◽  
pp. 3-14 ◽  
Author(s):  
Megan L. Porter ◽  
Joseph R. Blasic ◽  
Michael J. Bok ◽  
Evan G. Cameron ◽  
Thomas Pringle ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Large Scale ◽  
Current Model ◽  
Expression Patterns ◽  
Model Organisms ◽  
Biological Functions ◽  
Site Specific ◽  
History Of ◽  
Functional Features

Opsin proteins are essential molecules in mediating the ability of animals to detect and use light for diverse biological functions. Therefore, understanding the evolutionary history of opsins is key to understanding the evolution of light detection and photoreception in animals. As genomic data have appeared and rapidly expanded in quantity, it has become possible to analyse opsins that functionally and histologically are less well characterized, and thus to examine opsin evolution strictly from a genetic perspective. We have incorporated these new data into a large-scale, genome-based analysis of opsin evolution. We use an extensive phylogeny of currently known opsin sequence diversity as a foundation for examining the evolutionary distributions of key functional features within the opsin clade. This new analysis illustrates the lability of opsin protein-expression patterns, site-specific functionality (i.e. counterion position) and G-protein binding interactions. Further, it demonstrates the limitations of current model organisms, and highlights the need for further characterization of many of the opsin sequence groups with unknown function.

scholarly journals Deep time diversity and the early radiations of birds

2021 ◽  
Vol 118 (10) ◽  
pp. e2019865118
Author(s):  
Yilun Yu ◽  
Chi Zhang ◽  
Xing Xu
Keyword(s):  
Evolutionary History ◽  
Large Scale ◽  
Evolutionary Rate ◽  
Rapid Evolution ◽  
Morphological Data ◽  
Deep Time ◽  
The Third ◽  
Time Diversity ◽  
History Of

Reconstructing the history of biodiversity has been hindered by often-separate analyses of stem and crown groups of the clades in question that are not easily understood within the same unified evolutionary framework. Here, we investigate the evolutionary history of birds by analyzing three supertrees that combine published phylogenies of both stem and crown birds. Our analyses reveal three distinct large-scale increases in the diversification rate across bird evolutionary history. The first increase, which began between 160 and 170 Ma and reached its peak between 130 and 135 Ma, corresponds to an accelerated morphological evolutionary rate associated with the locomotory systems among early stem birds. This radiation resulted in morphospace occupation that is larger and different from their close dinosaurian relatives, demonstrating the occurrence of a radiation among early stem birds. The second increase, which started ∼90 Ma and reached its peak between 65 and 55 Ma, is associated with rapid evolution of the cranial skeleton among early crown birds, driven differently from the first radiation. The third increase, which occurred after ∼40 to 45 Ma, has yet to be supported by quantitative morphological data but gains some support from the fossil record. Our analyses indicate that the bird biodiversity evolution was influenced mainly by long-term climatic changes and also by major paleobiological events such as the Cretaceous–Paleogene (K–Pg) extinction.

Bioregionalisation of the freshwater zoogeographical areas of mainland China

Zootaxa ◽  
2020 ◽  
Vol 4742 (2) ◽  
pp. 271-298 ◽  
Author(s):  
CHAO HUANG ◽  
MALTE C. EBACH ◽  
SHANE T. AHYONG
Keyword(s):  
Large Scale ◽  
Quantitative Methods ◽  
Mainland China ◽  
Animal Group ◽  
Biogeographic Patterns ◽  
Network Analyses ◽  
Freshwater Crabs ◽  
Occurrence Data ◽  
History Of ◽  
Province Level

Biogeographic regionalisations extract patterns of co-occurrence from different taxa to form a hierarchical system of geographical units of different scales. This system is useful for revealing biogeographic patterns and can be used as the basis for scientific communication between different fields. The history of Chinese freshwater biogeography is not well known to most modern biogeographers and is reviewed herein. We produce the first quantitative bioregionalisation of the freshwater zoogeographic areas of mainland China based on multiple animal groups. The combined occurrence data of amphibians, freshwater fish and freshwater crabs were subjected to cluster and network analyses. The two different methods yielded largely similar results. We propose four freshwater zoogeographical subregions (Beifang, Tarim, China, and the Tibetan subregion), three dominions for the China subregion (Jianghuai, Dongyang, and the new Dian dominion), three provinces for the Dian dominion (West Hengduan, Diannan Highlands and the new Yungui Plateau province) and two provinces for the Dongyang dominion (Zhemin and the new Huanan province) according to the naming rules of ICAN. The endemic areas of each animal group were then individually studied and were found to reflect the bioregionalisation at the subregion level, but differed from each other at the dominion and province level. Our analyses show that: (1) previous intuitive biogeographical studies have found similar areas; (2) there are recurring large scale biogeographic patterns in Chinese freshwater fishes, amphibians and freshwater crabs; and (3) bioregionalisations derived from quantitative methods can be effective for partitioning areas into biogeographically meaningful units. 

scholarly journals Large-Scale Phylogenomic Analysis Reveals the Complex Evolutionary History of Rabies Virus in Multiple Carnivore Hosts

2016 ◽  
Vol 12 (12) ◽  
pp. e1006041 ◽  
Author(s):  
Cécile Troupin ◽  
Laurent Dacheux ◽  
Marion Tanguy ◽  
Claude Sabeta ◽  
Hervé Blanc ◽  
...  
Keyword(s):  
Rabies Virus ◽  
Evolutionary History ◽  
Large Scale ◽  
Phylogenomic Analysis ◽  
History Of ◽  
Complex Evolutionary History

scholarly journals Widespread introgression across a phylogeny of 155 Drosophila genomes

2020 ◽  
Author(s):  
Anton Suvorov ◽  
Bernard Y. Kim ◽  
Jeremy Wang ◽  
Ellie E. Armstrong ◽  
David Peede ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Sequence Data ◽  
Gene Tree ◽  
History Of ◽  
Mapping Gene ◽  
Gene Tree Discordance ◽  
Evolutionary Consequences ◽  
Genome Assemblies ◽  
Genome Scale ◽  
Hybridization And Introgression

Genome-scale sequence data has invigorated the study of hybridization and introgression, particularly in animals. However, outside of a few notable cases, we lack systematic tests for introgression at a larger phylogenetic scale across entire clades. Here we leverage 155 genome assemblies, from 149 species, to generate a fossil-calibrated phylogeny and conduct multilocus tests for introgression across 9 monophyletic radiations within the genus Drosophila. Using complementary phylogenomic approaches, we identify widespread introgression across the evolutionary history of Drosophila. Mapping gene-tree discordance onto the phylogeny revealed that both ancient and recent introgression has occurred, with introgression at the base of species radiations being particularly common. Our results provide the first evidence of introgression occurring across the evolutionary history of Drosophila and highlight the need to continue to study the evolutionary consequences of hybridization and introgression in this genus and across the Tree of Life.

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