scholarly journals The Evolution of Sex is Tempered by Costly Hybridization in Boechera (Rock Cress)

2020 ◽  
Author(s):  
Catherine A Rushworth ◽  
Tom Mitchell-Olds
Keyword(s):  
Reproductive Isolation ◽  
Evolutionary Biology ◽  
Ecological Model ◽  
De Novo ◽  
Hybrid Sterility ◽  
Reproductive Mode ◽  
Evolution Of Sex ◽  
Widespread Species ◽  
Fitness Consequences ◽  
In The Wild

Abstract Despite decades of research, the evolution of sex remains an enigma in evolutionary biology. Typically, research addresses the costs of sex and asexuality to characterize the circumstances favoring one reproductive mode. Surprisingly few studies address the influence of common traits that are, in many organisms, obligately correlated with asexuality, including hybridization and polyploidy. These characteristics have substantial impacts on traits under selection. In particular, the fitness consequences of hybridization (i.e., reduced fitness due to interspecific reproductive isolation) will influence the evolution of sex. This may comprise a cost of either sex or asexuality due to the link between hybridity and asexuality. We examined reproductive isolation in the formation of de novo hybrid lineages between 2 widespread species in the ecological model system Boechera. Seventeen percent of 664 crosses produced F1 fruits, and only 10% of these were viable, suggesting that postmating prezygotic and postzygotic barriers inhibit hybrid success in this system. The postmating prezygotic barrier was asymmetrical, with 110 of 115 total F1 fruits produced when Boechera stricta acted as maternal parent. This asymmetry was confirmed in wild-collected lineages, using a chloroplast phylogeny of wild-collected B. stricta, Boechera retrofracta, and hybrids. We next compared fitness of F2 hybrids and selfed parental B. stricta lines, finding that F2 fitness was reduced by substantial hybrid sterility. Multiple reproductively isolating barriers influence the formation and fitness of hybrid lineages in the wild, and the costs of hybridization likely have profound impacts on the evolution of sex in the natural environment.

scholarly journals The evolution of sex is tempered by costly hybridization in Boechera (rock cress)

2020 ◽  
Author(s):  
Catherine A. Rushworth ◽  
Tom Mitchell-Olds
Keyword(s):  
Evolutionary Biology ◽  
Ecological Model ◽  
De Novo ◽  
Hybrid Sterility ◽  
Evolution Of Sex ◽  
Widespread Species ◽  
Major Barrier ◽  
Chloroplast Haplotype ◽  
In The Wild ◽  
Boechera Stricta

AbstractEven after decades of research, the evolution of sex remains an enigma in evolutionary biology. Typically, research addresses the costs of sex and asexuality to characterize the circumstances in which one reproductive system is more favorable. Yet surprisingly few studies address the influence of common traits that are obligately correlated with asexuality, including hybridization and polyploidy; even though these traits have substantial impacts on selective patterns. In particular, hybridization is well-known to alter trait expression; these alterations may themselves represent a cost of sex. We examined the role of reproductive isolation in the formation of de novo hybrid lineages between two widespread species in the ecological model system Boechera. Of 664 crosses between Boechera stricta and Boechera retrofracta, 17% of crosses produced F1 fruits. This suggests that postmating prezygotic barriers, i.e. pollen-pistil interactions, form the major barrier to hybrid success in this system. These interactions are asymmetrical, with 110 F1 fruits produced when B. stricta was the maternal parent. This asymmetry was confirmed using a chloroplast phylogeny of wild-collected B. stricta, B. retrofracta, and hybrids, which showed that most hybrids have a B. stricta chloroplast haplotype. We next compared fitness of F2 hybrids and selfed parental B. stricta lines, finding that F2 fitness was reduced by substantial hybrid sterility. Our results suggest that multiple reproductively isolating barriers likely influence the formation and fitness of hybrid lineages in the wild, and that these costs of hybridization likely have profound impacts on the costs of sex in the natural environment.

scholarly journals Independent domestications shape the genetic pattern of a reproductive isolation system in rice

2020 ◽  
Author(s):  
Xun Xu ◽  
Song Ge ◽  
Fu-Min Zhang
Keyword(s):  
Reproductive Isolation ◽  
Hybrid Sterility ◽  
Cost Savings ◽  
Isolation System ◽  
Bottleneck Effect ◽  
In The Wild ◽  
History Of ◽  
On Line ◽  
Selection For ◽  
Sterility Genes

AbstractSevere reproductive isolation (RI) exists between the two subspecies of rice, Indica and Japonica, but in the wild ancestors no post-zygotic RI was found. The studies about the establishment of the interspecies RI of rice are still rear. A pair of rice hybrid sterility genes, DOPPELGANGER 1 (DPL1) and DOPPELGANGER 2 (DPL2), offers a convenient example to study the evolutionary history of RI genes. Either of the two loci has one non-functional allele (DPL1- and DPL2-). The hybrid pollen carrying both DPL1- and DPL2- will be sterility.We collected 811 individuals: Oryza sativa (132), the two wild ancestors O. nivara (296) and O. rufipogon (383) as well as 20 DPL1 and 34 DPL2 sequences of O. sativa from on-line databases. We analysed the genetic and geographic pattern of DPLs in all three species to determine the origination regions of DPL1- and DPL2-. The neutral test as well as the diversities of nucleotide and haplotype were used to detect if selection shaped the pattern of DPLs.We found that DPL1- and DPL2- of rice emerged from wild ancestor populations in South Asia and South China through two respective domestications. Comparing with the ancestral populations, DPL1- and DPL2- both showed reduce of diversities, however their frequencies increased in rice. We assume that the reduce of diversities due to the bottleneck effect of domestication while the loss of one copy was preferred by artificial selection for cost savings.

scholarly journals De Novo Genome Assemblies for Three North American Bumble Bee Species: Bombus bifarius, Bombus vancouverensis, and Bombus vosnesenskii

2020 ◽  
Vol 10 (8) ◽  
pp. 2585-2592
Author(s):  
Sam D. Heraghty ◽  
John M. Sutton ◽  
Meaghan L. Pimsler ◽  
Janna L. Fierst ◽  
James P. Strange ◽  
...  
Keyword(s):  
Evolutionary Biology ◽  
De Novo ◽  
Bombus Terrestris ◽  
Bumble Bee ◽  
Hybrid Assembly ◽  
Widespread Species ◽  
Oxford Nanopore ◽  
Genome Assemblies ◽  
High Degree ◽  
Oxford Nanopore Technologies

Bumble bees are ecologically and economically important insect pollinators. Three abundant and widespread species in western North America, Bombus bifarius, Bombus vancouverensis, and Bombus vosnesenskii, have been the focus of substantial research relating to diverse aspects of bumble bee ecology and evolutionary biology. We present de novo genome assemblies for each of the three species using hybrid assembly of Illumina and Oxford Nanopore Technologies sequences. All three assemblies are of high quality with large N50s (> 2.2 Mb), BUSCO scores indicating > 98% complete genes, and annotations producing 13,325 – 13,687 genes, comparing favorably with other bee genomes. Analysis of synteny against the most complete bumble bee genome, Bombus terrestris, reveals a high degree of collinearity. These genomes should provide a valuable resource for addressing questions relating to functional genomics and evolutionary biology in these species.

scholarly journals Venom-gland transcriptomic, venomic, and antivenomic profiles of the spine-bellied sea snake (Hydrophis curtus) from the South China Sea

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Hong-Yan Zhao ◽  
Lin Wen ◽  
Yu-Feng Miao ◽  
Yu Du ◽  
Yan Sun ◽  
...  
Keyword(s):  
South China Sea ◽  
South China ◽  
Evolutionary History ◽  
De Novo ◽  
Venom Gland ◽  
The South China Sea ◽  
Protein Families ◽  
The South ◽  
Widespread Species ◽  
China Sea

Abstract Background A comprehensive evaluation of the -omic profiles of venom is important for understanding the potential function and evolution of snake venom. Here, we conducted an integrated multi-omics-analysis to unveil the venom-transcriptomic and venomic profiles in a same group of spine-bellied sea snakes (Hydrophis curtus) from the South China Sea, where the snake is a widespread species and might generate regionally-specific venom potentially harmful to human activities. The capacity of two heterologous antivenoms to immunocapture the H. curtus venom was determined for an in-depth evaluation of their rationality in treatment of H. curtus envenomation. In addition, a phylogenetic analysis by maximum likelihood was used to detect the adaptive molecular evolution of full-length toxin-coding unigenes. Results A total of 90,909,384 pairs of clean reads were generated via Illumina sequencing from a pooled cDNA library of six specimens, and yielding 148,121 unigenes through de novo assembly. Sequence similarity searching harvested 63,845 valid annotations, including 63,789 non-toxin-coding and 56 toxin-coding unigenes belonging to 22 protein families. Three protein families, three-finger toxins (3-FTx), phospholipase A2 (PLA2), and cysteine-rich secretory protein, were detected in the venom proteome. 3-FTx (27.15% in the transcriptome/41.94% in the proteome) and PLA2 (59.71%/49.36%) were identified as the most abundant families in the venom-gland transcriptome and venom proteome. In addition, 24 unigenes from 11 protein families were shown to have experienced positive selection in their evolutionary history, whereas four were relatively conserved throughout evolution. Commercial Naja atra antivenom exhibited a stronger capacity than Bungarus multicinctus antivenom to immunocapture H. curtus venom components, especially short neurotoxins, with the capacity of both antivenoms to immunocapture short neurotoxins being weaker than that for PLA2s. Conclusions Our study clarified the venom-gland transcriptomic and venomic profiles along with the within-group divergence of a H. curtus population from the South China Sea. Adaptive evolution of most venom components driven by natural selection appeared to occur rapidly during evolutionary history. Notably, the utility of commercial N. atra and B. multicinctus antivenoms against H. curtus toxins was not comprehensive; thus, the development of species-specific antivenom is urgently needed.

scholarly journals The Rubisco small subunits in the green algal genus Chloromonas provide insights into evolutionary loss of the eukaryotic carbon-concentrating organelle, the pyrenoid

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Ryo Matsuzaki ◽  
Shigekatsu Suzuki ◽  
Haruyo Yamaguchi ◽  
Masanobu Kawachi ◽  
Yu Kanesaki ◽  
...  
Keyword(s):  
Evolutionary Biology ◽  
De Novo ◽  
Small Subunit ◽  
Plant Evolution ◽  
Reaction Products ◽  
Photosynthetic Organisms ◽  
Green Algal ◽  
Interesting Study ◽  
Algal Genus ◽  
The Relationship

Abstract Background Pyrenoids are protein microcompartments composed mainly of Rubisco that are localized in the chloroplasts of many photosynthetic organisms. Pyrenoids contribute to the CO2-concentrating mechanism. This organelle has been lost many times during algal/plant evolution, including with the origin of land plants. The molecular basis of the evolutionary loss of pyrenoids is a major topic in evolutionary biology. Recently, it was hypothesized that pyrenoid formation is controlled by the hydrophobicity of the two helices on the surface of the Rubisco small subunit (RBCS), but the relationship between hydrophobicity and pyrenoid loss during the evolution of closely related algal/plant lineages has not been examined. Here, we focused on, the Reticulata group of the unicellular green algal genus Chloromonas, within which pyrenoids are present in some species, although they are absent in the closely related species. Results Based on de novo transcriptome analysis and Sanger sequencing of cloned reverse transcription-polymerase chain reaction products, rbcS sequences were determined from 11 strains of two pyrenoid-lacking and three pyrenoid-containing species of the Reticulata group. We found that the hydrophobicity of the RBCS helices was roughly correlated with the presence or absence of pyrenoids within the Reticulata group and that a decrease in the hydrophobicity of the RBCS helices may have primarily caused pyrenoid loss during the evolution of this group. Conclusions Although we suggest that the observed correlation may only exist for the Reticulata group, this is still an interesting study that provides novel insight into a potential mechanism determining initial evolutionary steps of gain and loss of the pyrenoid.

scholarly journals De Novo Development of mtDNA Deletion Due to Decreased POLG and SSBP1 Expression in Humans

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 284
Author(s):  
Yeonmi Lee ◽  
Taeho Kim ◽  
Miju Lee ◽  
Seongjun So ◽  
Mustafa Zafer Karagozlu ◽  
...  
Keyword(s):  
Dna Polymerase ◽  
De Novo ◽  
Wild Type Allele ◽  
Wild Type ◽  
Factors Associated ◽  
Mtdna Deletions ◽  
Nuclear Factors ◽  
Mtdna Deletion ◽  
In The Wild ◽  
Mtdna Replication

Defects in the mitochondrial genome (mitochondrial DNA (mtDNA)) are associated with both congenital and acquired disorders in humans. Nuclear-encoded DNA polymerase subunit gamma (POLG) plays an important role in mtDNA replication, and proofreading and mutations in POLG have been linked with increased mtDNA deletions. SSBP1 is also a crucial gene for mtDNA replication. Here, we describe a patient diagnosed with Pearson syndrome with large mtDNA deletions that were not detected in the somatic cells of the mother. Exome sequencing was used to evaluate the nuclear factors associated with the patient and his family, which revealed a paternal POLG mutation (c.868C > T) and a maternal SSBP1 mutation (c.320G > A). The patient showed lower POLG and SSBP1 expression than his healthy brothers and the general population of a similar age. Notably, c.868C in the wild-type allele was highly methylated in the patient compared to the same site in both his healthy brothers. These results suggest that the co- deficient expression of POLG and SSBP1 genes could contribute to the development of mtDNA deletion.

scholarly journals Contingency in the convergent evolution of a regulatory network: Dosage compensation in Drosophila

2018 ◽  
Author(s):  
Doris Bachtrog ◽  
Chris Ellison
Keyword(s):  
Transposable Element ◽  
Dosage Compensation ◽  
Sex Chromosomes ◽  
Binding Sites ◽  
Evolutionary Biology ◽  
De Novo ◽  
Binding Motif ◽  
Sequence Motif ◽  
X Chromosomes ◽  
Msl Complex

The repeatability or predictability of evolution is a central question in evolutionary biology, and most often addressed in experimental evolution studies. Here, we infer how genetically heterogeneous natural systems acquire the same molecular changes, to address how genomic background affects adaptation in natural populations. In particular, we take advantage of independently formed neo-sex chromosomes in Drosophila species that have evolved dosage compensation by co-opting the dosage compensation (MSL) complex, to study the mutational paths that have led to the acquisition of 100s of novel binding sites for the MSL complex in different species. This complex recognizes a conserved 21-bp GA-rich sequence motif that is enriched on the X chromosome, and newly formed X chromosomes recruit the MSL complex by de novo acquisition of this binding motif. We identify recently formed sex chromosomes in the Drosophila repleta and robusta species groups by genome sequencing, and generate genomic occupancy maps of the MSL complex to infer the location of novel binding sites. We find that diverse mutational paths were utilized in each species to evolve 100s of de novo binding motifs along the neo-X, including expansions of microsatellites and transposable element insertions. However, the propensity to utilize a particular mutational path differs between independently formed X chromosomes, and appears to be contingent on genomic properties of that species, such as simple repeat or transposable element density. This establishes the “genomic environment” as an important determinant in predicting the outcome of evolutionary adaptations.

A CYC-RAD-DIV-DRIF interaction likely pre-dates the origin of floral monosymmetry in Lamiales

2021 ◽  
Author(s):  
Aniket Sengupta ◽  
Lena C. Hileman
Keyword(s):  
Evolutionary Biology ◽  
De Novo ◽  
Tomato Fruit ◽  
Regulatory Interaction ◽  
En Bloc ◽  
Regulatory Interactions ◽  
Developmental Program ◽  
Novel Traits ◽  
Carpel Development ◽  
Outstanding Question

Abstract BackgroundAn outstanding question in evolutionary biology is how genetic interactions defining novel traits evolve. They may evolve either by de novo assembly of previously non-interacting genes or by en bloc co-option of interactions from other functions. We tested these hypotheses in the context of a novel phenotype—Lamiales flower monosymmetry—defined by a developmental program that relies on regulatory interaction among CYCLOIDEA , RADIALIS , DIVARICATA , and DRIF gene products. In Antirrhinum majus (snapdragon), representing Lamiales, we tested whether components of this program likely function beyond their previously known role in petal and stamen development. In Solanum lycopersicum (tomato), representing Solanales which diverged from Lamiales before the origin of Lamiales floral monosymmetry, we additionally tested for regulatory interactions in this program. ResultsWe found that RADIALIS , DIVARICATA , and DRIF are expressed in snapdragon ovaries and developing fruit, similar to their homologs during tomato fruit development. Additionally, we found that a tomato CYCLOIDEA ortholog positively regulates a tomato RADIALIS ortholog. ConclusionOur results provide preliminary support to the hypothesis that the developmental program defining floral monosymmetry in Lamiales was co-opted en bloc from a function in carpel development. This expands our understanding of novel trait evolution facilitated by co-option of existing regulatory interactions.

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