scholarly journals Introgressive hybridization facilitates adaptive divergence in a recent radiation of monkeyflowers

2015 ◽  
Vol 282 (1814) ◽  
pp. 20151666 ◽  
Author(s):  
Sean Stankowski ◽  
Matthew A. Streisfeld

A primary goal in evolutionary biology is to identify the historical events that have facilitated the origin and spread of adaptations. When these adaptations also lead to reproductive isolation, we can learn about the evolutionary mechanisms contributing to speciation. We reveal the complex history of the gene MaMyb2 in shaping flower colour divergence within a recent radiation of monkeyflowers. In the Mimulus aurantiacus species complex, red-flowered M. a. ssp . puniceus and yellow-flowered M. a. ssp. australis are partially isolated because of differences in pollinator preferences. Phylogenetic analyses based on genome-wide variation across the complex suggest two origins of red flowers from a yellow-flowered ancestor: one in M. a. ssp . puniceus and one in M. a. ssp. flemingii . However, in both cases, red flowers are caused by cis -regulatory mutations in the gene MaMyb2 . Although this could be due to distinct mutations in each lineage, we show that the red allele in M. a. ssp. puniceus did not evolve de novo or exist as standing variation in its yellow-flowered ancestor. Rather, our results suggest that a single red MaMyb2 allele evolved during the radiation of M. aurantiacus that was subsequently transferred to the yellow-flowered ancestor of M. a. ssp. puniceus via introgressive hybridization. Because gene flow is still possible among taxa, we conclude that introgressive hybridization can be a potent driver of adaptation at the early stages of divergence that can contribute to the origins of biodiversity.

2020 ◽  
Vol 37 (5) ◽  
pp. 1295-1305 ◽  
Author(s):  
Sean P Mullen ◽  
Nicholas W VanKuren ◽  
Wei Zhang ◽  
Sumitha Nallu ◽  
Evan B Kristiansen ◽  
...  

Abstract Understanding the origin and maintenance of adaptive phenotypic novelty is a central goal of evolutionary biology. However, both hybridization and incomplete lineage sorting can lead to genealogical discordance between the regions of the genome underlying adaptive traits and the remainder of the genome, decoupling inferences about character evolution from population history. Here, to disentangle these effects, we investigated the evolutionary origins and maintenance of Batesian mimicry between North American admiral butterflies (Limenitis arthemis) and their chemically defended model (Battus philenor) using a combination of de novo genome sequencing, whole-genome resequencing, and statistical introgression mapping. Our results suggest that balancing selection, arising from geographic variation in the presence or absence of the unpalatable model, has maintained two deeply divergent color patterning haplotypes that have been repeatedly sieved among distinct mimetic and nonmimetic lineages of Limenitis via introgressive hybridization.


2020 ◽  
Vol 59 (1) ◽  
pp. e02198-20
Author(s):  
N. Effelsberg ◽  
M. Stegger ◽  
L. Peitzmann ◽  
O. Altinok ◽  
G. W. Coombs ◽  
...  

ABSTRACTStaphylococcus aureus ST45 is a major global MRSA lineage with huge strain diversity and a high clinical impact. It is one of the most prevalent carrier lineages but also frequently causes severe invasive disease, such as bacteremia. Little is known about its evolutionary history. In this study, we used whole-genome sequencing to analyze a large collection of 451 diverse ST45 isolates from 6 continents and 26 countries. De novo-assembled genomes were used to understand genomic plasticity and to perform coalescent analyses. The ST45 population contained two distinct sublineages, which correlated with the isolates’ geographical origins. One sublineage primarily consisted of European/North American isolates, while the second sublineage primarily consisted of African and Australian isolates. Bayesian analysis predicted ST45 originated in northwestern Europe about 500 years ago. Isolation time, host, and clinical symptoms did not correlate with phylogenetic groups. Our phylogenetic analyses suggest multiple acquisitions of the SCCmec element and key virulence factors throughout the evolution of the ST45 lineage.


Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 2425-2425 ◽  
Author(s):  
Davide Rossi ◽  
Valeria Spina ◽  
Daniela Capello ◽  
Francesco Forconi ◽  
Maurizio Martini ◽  
...  

Abstract Abstract 2425 Mechanisms promoting chronic lymphocytic leukemia (CLL) transformation to Richter syndrome (RS) are poorly understood and might involve antigen stimulation. We explored intraclonal diversification (ID) of immunoglobulin (IGHV) genes in RS in order to: i) follow the evolutionary history of the RS tumor clone over time; ii) understand whether antigen stimulation sustains the growth of DLBCL cells once RS is established. The study was based on 11 clonally related CLL/RS pairs, 7 clonally unrelated RS, and, for comparison, 20 de novo DLBCL. Fifty IGHV subclones were analysed per sample. Mutations observed in only one subclone were defined unconfirmed (UCM). Partially shared mutations were defined confirmed (CM). Cases were scored positive for ID only in the presence of confirmed mutations. For each sample, the normalized mutation frequency (NMF) of ongoing somatic hypermutation was calculated. Phylogenetic analyses was performed with MEGA4. Most (10/11, 90.9%) clonally related RS originated from an ancestor clone that was already present at the time of CLL diagnosis (Fig 1A, 1B, 1C). One single RS case had a transformation pattern compatible with sequential evolution from a secondary CLL subclone (Fig. 1D). All secondary CLL subclones that were documented in the CLL phase disappeared once transformation had occurred, and were substituted by the dominant DLBCL clone with its own descendants. Paired analsysis of clonally related CLL/RS samples documented that NMF significantly decreased during evolution from the CLL phase (median: 0.76 × 10−3) to the RS phase (median: 0.13 × 10−3)(p=.013). Accordingly, at transformation, the ID of IGHV genes switched off in 6/11 (54.5%) clonally related CLL/RS pairs. Clonally related RS that upon transformation maintained ID of IGHV genes were characterized by a higher prevalence of aberrant somatic hypermutation of proto-oncogenes compared to cases lacking ID (0/6 vs 3/4, 75.0%, respectively; p=.033). Also, RS cases that maintained ID of IGHV genes acquired more frequently c-MYC translocation at the time of transformation (0/6 vs 2/4, respectively; p=.133). Clonally unrelated RS are characterized by the development of a de novo DLBCL in the context of CLL. Despite morphologic and phenotypic similarities, clonally unrelated RS differed from de novo DLBCL in terms of NMF (median: 1.18 × 10−3 range: vs median: 0.08 × 10−3 range, respectively; p=.016) and prevalence of cases harboring ID (6/7, 85.7% vs 6/20, 30.0%, respectively; p=.024). The NMF was also significantly higher in clonally unrelated RS compared to clonally related cases (p=.001). These data indicate that: i) RS transformation is due to the expansion of a common ancestor clone that gains selective advantage over other subclones of the CLL phase; ii) antigen stimulation exerts different roles in clonally related RS, clonally unrelated RS and de novo DLBCL; iii) more than 50% clonally related RS switched off ID at the time of transformation, suggesting that the DLBCL clone has become independent of antigen stimulation for its sustainment; iv) clonally related RS that maintained ID of IGHV genes at transformation may take advantage of ID as a mechanism for accumulating genetic instability. Disclosures: No relevant conflicts of interest to declare.


Genome ◽  
2017 ◽  
Vol 60 (9) ◽  
pp. 733-742 ◽  
Author(s):  
John D. McVay ◽  
Duncan Hauser ◽  
Andrew L. Hipp ◽  
Paul S. Manos

Species within the genus Quercus (oak) hybridize in complex patterns that have yet to be fully explored with phylogenomic data. Analyses to date have recovered reasonable divergent patterns, suggesting that the impact of introgression may not always be obvious in inferred oak phylogenies. We explore this phenomenon using RADseq data for 136 samples representing 54 oak species by conducting phylogenetic analyses designed to distinguish signals of lineage diversification and hybridization, focusing on the lobed-leaf species Quercus gambelii, Q. lobata, and Q. garryana in the context of a broad sampling of allied white oaks (Quercus section Quercus), and particularly the midwestern Q. macrocarpa. We demonstrate that historical introgressive hybridization between once sympatric species affects phylogeny estimation. Historical range expansion during periods of favorable climate likely explains our observations; analyses support genetic exchange between ancestral populations of Q. gambelii and Q. macrocarpa. We conclude that the genomic consequences of introgression caused the attraction of distant lineages in phylogenetic tree space, and that introgressive and divergent signals can be disentangled to produce a robust estimate of the phylogenetic history of the species.


2021 ◽  
Vol 12 ◽  
Author(s):  
Mi-Jeong Yoo ◽  
Byoung-Yoon Lee ◽  
Sangtae Kim ◽  
Chae Eun Lim

The genus Hosta (Agavoideae and Asparagaceae) is one of the most popular landscaping and ornamental plants native to temperate East Asia. Their popularity has led to extensive hybridization to develop various cultivars. However, their long history of hybridization, cultivation, and selection has brought about taxonomic confusion in the Hosta species delimitation along with their indistinguishable morphology. Here, we conducted the first broad phylogenetic analyses of Hosta species based on the most comprehensive genomic data set to date. To do so, we captured 246 nuclear gene sequences and plastomes from 55 accessions of Korean Hosta species using the Hyb-Seq method. As a result, this study provides the following novel and significant findings: (1) phylogenetic analyses of the captured sequences retrieved six species of Hosta in South Korea compared to five to eleven species based on the previous studies, (2) their phylogenetic relationships suggested that the large genome size was ancestral and the diversification of Korean Hosta species was accompanied by decreases in genome sizes, (3) comparison between nuclear genes and plastome revealed several introgressive hybridization events between Hosta species, and (4) divergence times estimated here showed that Hosta diverged 35.59 million years ago, while Korean Hosta species rapidly diversified during the late Miocene. Last, we explored whether these genomic data could be used to infer the origin of cultivars. In summary, this study provides the most comprehensive genomic resources to be used in phylogenetic, population, and conservation studies of Hosta, as well as for unraveling the origin of many cultivars.


Plants ◽  
2020 ◽  
Vol 9 (6) ◽  
pp. 737 ◽  
Author(s):  
Abdullah ◽  
Claudia L. Henriquez ◽  
Furrukh Mehmood ◽  
Iram Shahzadi ◽  
Zain Ali ◽  
...  

The chloroplast genome provides insight into the evolution of plant species. We de novo assembled and annotated chloroplast genomes of four genera representing three subfamilies of Araceae: Lasia spinosa (Lasioideae), Stylochaeton bogneri, Zamioculcas zamiifolia (Zamioculcadoideae), and Orontium aquaticum (Orontioideae), and performed comparative genomics using these chloroplast genomes. The sizes of the chloroplast genomes ranged from 163,770 bp to 169,982 bp. These genomes comprise 113 unique genes, including 79 protein-coding, 4 rRNA, and 30 tRNA genes. Among these genes, 17–18 genes are duplicated in the inverted repeat (IR) regions, comprising 6–7 protein-coding (including trans-splicing gene rps12), 4 rRNA, and 7 tRNA genes. The total number of genes ranged between 130 and 131. The infA gene was found to be a pseudogene in all four genomes reported here. These genomes exhibited high similarities in codon usage, amino acid frequency, RNA editing sites, and microsatellites. The oligonucleotide repeats and junctions JSB (IRb/SSC) and JSA (SSC/IRa) were highly variable among the genomes. The patterns of IR contraction and expansion were shown to be homoplasious, and therefore unsuitable for phylogenetic analyses. Signatures of positive selection were seen in three genes in S. bogneri, including ycf2, clpP, and rpl36. This study is a valuable addition to the evolutionary history of chloroplast genome structure in Araceae.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Mingzheng Duan ◽  
Haiying Bao ◽  
Tolgor Bau

AbstractIn this study, we report a de novo assembly of the first high-quality genome for a wild mushroom species Leucocalocybe mongolica (LM). We performed high-throughput transcriptome sequencing to analyze the genetic basis for the life history of LM. Our results show that the genome size of LM is 46.0 Mb, including 26 contigs with a contig N50 size of 3.6 Mb. In total, we predicted 11,599 protein-coding genes, of which 65.7% (7630) could be aligned with high confidence to annotated homologous genes in other species. We performed phylogenetic analyses using genes form 3269 single-copy gene families and showed support for distinguishing LM from the genus Tricholoma (L.) P.Kumm., in which it is sometimes circumscribed. We believe that one reason for limited wild occurrences of LM may be the loss of key metabolic genes, especially carbohydrate-active enzymes (CAZymes), based on comparisons with other closely related species. The results of our transcriptome analyses between vegetative (mycelia) and reproductive (fruiting bodies) organs indicated that changes in gene expression among some key CAZyme genes may help to determine the switch from asexual to sexual reproduction. Taken together, our genomic and transcriptome data for LM comprise a valuable resource for both understanding the evolutionary and life history of this species.


2021 ◽  
Vol 118 (20) ◽  
pp. e2011811118
Author(s):  
Emilie J. Richards ◽  
Joseph A. McGirr ◽  
Jeremy R. Wang ◽  
Michelle E. St. John ◽  
Jelmer W. Poelstra ◽  
...  

To investigate the origins and stages of vertebrate adaptive radiation, we reconstructed the spatial and temporal histories of adaptive alleles underlying major phenotypic axes of diversification from the genomes of 202 Caribbean pupfishes. On a single Bahamian island, ancient standing variation from disjunct geographic sources was reassembled into new combinations under strong directional selection for adaptation to the novel trophic niches of scale-eating and molluscivory. We found evidence for two longstanding hypotheses of adaptive radiation: hybrid swarm origins and temporal stages of adaptation. Using a combination of population genomics, transcriptomics, and genome-wide association mapping, we demonstrate that this microendemic adaptive radiation of novel trophic specialists on San Salvador Island, Bahamas experienced twice as much adaptive introgression as generalist populations on neighboring islands and that adaptive divergence occurred in stages. First, standing regulatory variation in genes associated with feeding behavior (prlh, cfap20, and rmi1) were swept to fixation by selection, then standing regulatory variation in genes associated with craniofacial and muscular development (itga5, ext1, cyp26b1, and galr2) and finally the only de novo nonsynonymous substitution in an osteogenic transcription factor and oncogene (twist1) swept to fixation most recently. Our results demonstrate how ancient alleles maintained in distinct environmental refugia can be assembled into new adaptive combinations and provide a framework for reconstructing the spatiotemporal landscape of adaptation and speciation.


2021 ◽  
Author(s):  
Marlene Haider ◽  
Martin P. Schilling ◽  
Markus H. Moest ◽  
Florian M. Steiner ◽  
Birgit C. Schlick-Steiner ◽  
...  

AbstractReconstruction of species histories is a central aspect of evolutionary biology. Patterns of genetic variation within and among populations can be leveraged to elucidate evolutionary processes and demographic histories. However, interpreting genetic signatures and unraveling the contributing processes can be challenging, in particular for non-model organisms with complex reproductive modes and genome organization. One way forward is the combined consideration of patterns revealed by different molecular markers (nuclear vs. mitochondrial) and types of variants (common vs. rare) that differ in their age, mode and rate of evolution. Here, we applied this approach to Machilis pallida (Archaeognatha), an Alpine jumping bristletail considered parthenogenetic and triploid. We generated de-novo transcriptome and mitochondrial assemblies to obtain high-density data to investigate patterns of mitochondrial and common and rare nuclear variation in 17 M. pallida individuals sampled across the Alps from all known populations. We find that the different variant types capture distinct aspects of the evolutionary history and discuss the observed patterns in the context of parthenogenesis, polyploidy and survival during glaciation. This study highlights the potential of different variant types to unravel complex evolutionary scenarios and the suitability of M. pallida and the genus Machilis as a study system for the evolution of sexual strategies and polyploidization during environmental change. We also emphasize the need for further research which will be stimulated and facilitated by these newly generated resources and insights.


2019 ◽  
Vol 36 (10) ◽  
pp. 2227-2237 ◽  
Author(s):  
Anthony V Signore ◽  
Ying-Zhong Yang ◽  
Quan-Yu Yang ◽  
Ga Qin ◽  
Hideaki Moriyama ◽  
...  

Abstract A key question in evolutionary biology concerns the relative importance of different sources of adaptive genetic variation, such as de novo mutations, standing variation, and introgressive hybridization. A corollary question concerns how allelic variants derived from these different sources may influence the molecular basis of phenotypic adaptation. Here, we use a protein-engineering approach to examine the phenotypic effect of putatively adaptive hemoglobin (Hb) mutations in the high-altitude Tibetan wolf that were selectively introgressed into the Tibetan mastiff, a high-altitude dog breed that is renowned for its hypoxia tolerance. Experiments revealed that the introgressed coding variants confer an increased Hb–O2 affinity in conjunction with an enhanced Bohr effect. We also document that affinity-enhancing mutations in the β-globin gene of Tibetan wolf were originally derived via interparalog gene conversion from a tandemly linked β-globin pseudogene. Thus, affinity-enhancing mutations were introduced into the β-globin gene of Tibetan wolf via one form of intragenomic lateral transfer (ectopic gene conversion) and were subsequently introduced into the Tibetan mastiff genome via a second form of lateral transfer (introgression). Site-directed mutagenesis experiments revealed that the increased Hb–O2 affinity requires a specific two-site combination of amino acid replacements, suggesting that the molecular underpinnings of Hb adaptation in Tibetan mastiff (involving mutations that arose in a nonexpressed gene and which originally fixed in Tibetan wolf) may be qualitatively distinct from functionally similar changes in protein function that could have evolved via sequential fixation of de novo mutations during the breed’s relatively short duration of residency at high altitude.


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