scholarly journals Disentangling Population History and Character Evolution among Hybridizing Lineages

2020 ◽  
Vol 37 (5) ◽  
pp. 1295-1305 ◽  
Author(s):  
Sean P Mullen ◽  
Nicholas W VanKuren ◽  
Wei Zhang ◽  
Sumitha Nallu ◽  
Evan B Kristiansen ◽  
...  
Keyword(s):  
Evolutionary Biology ◽  
De Novo ◽  
Balancing Selection ◽  
Incomplete Lineage Sorting ◽  
Introgressive Hybridization ◽  
Character Evolution ◽  
Population History ◽  
Lineage Sorting ◽  
Evolutionary Origins ◽  
Whole Genome Resequencing

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.

scholarly journals Dissecting the basis of novel trait evolution in a radiation with widespread phylogenetic discordance

2017 ◽  
Author(s):  
Meng Wu ◽  
Jamie L. Kostyun ◽  
Matthew W. Hahn ◽  
Leonie Moyle
Keyword(s):  
De Novo ◽  
Incomplete Lineage Sorting ◽  
Phylogenetic Analyses ◽  
Gene Tree ◽  
Fruit Color ◽  
Species Tree ◽  
Color Variation ◽  
Lineage Sorting ◽  
Floral Character ◽  
Trait Evolution

ABSTRACTPhylogenetic analyses of trait evolution can provide insight into the evolutionary processes that initiate and drive phenotypic diversification. However, recent phylogenomic studies have revealed extensive gene tree-species tree discordance, which can lead to incorrect inferences of trait evolution if only a single species tree is used for analysis. This phenomenon—dubbed “hemiplasy”—is particularly important to consider during analyses of character evolution in rapidly radiating groups, where discordance is widespread. Here we generate whole-transcriptome data for a phylogenetic analysis of 14 species in the plant genus Jaltomata (the sister clade to Solanum), which has experienced rapid, recent trait evolution, including in fruit and nectar color, and flower size and shape. Consistent with other radiations, we find evidence for rampant gene tree discordance due to incomplete lineage sorting (ILS) and several introgression events among the well-supported subclades. Since both ILS and introgression increase the probability of hemiplasy, we perform several analyses that take discordance into account while identifying genes that might contribute to phenotypic evolution. Despite discordance, the history of fruit color evolution in Jaltomata can be inferred with high confidence, and we find evidence of de novo adaptive evolution at individual genes associated with fruit color variation. In contrast, hemiplasy appears to strongly affect inferences about floral character transitions in Jaltomata, and we identify candidate loci that could arise either from multiple lineage-specific substitutions or standing ancestral polymorphisms. Our analysis provides a generalizable example of how to manage discordance when identifying loci associated with trait evolution in a radiating lineage.

scholarly journals Comparative Performance of Popular Methods for Hybrid Detection using Genomic Data

2020 ◽  
Author(s):  
Sungsik Kong ◽  
Laura S. Kubatko
Keyword(s):  
Statistical Power ◽  
Evolutionary Dynamics ◽  
Mean Squared Error ◽  
Incomplete Lineage Sorting ◽  
Introgressive Hybridization ◽  
Genomic Data ◽  
Lineage Sorting ◽  
Comparative Performance ◽  
Pattern Frequency ◽  
Hybrid Detection

AbstractInterspecific hybridization is an important evolutionary phenomenon that generates genetic variability in a population and fosters species diversity in nature. The availability of large genome scale datasets has revolutionized hybridization studies to shift from the examination of the presence or absence of hybrids in nature to the investigation of the genomic constitution of hybrids and their genome-specific evolutionary dynamics. Although a handful of methods have been proposed in an attempt to identify hybrids, accurate detection of hybridization from genomic data remains a challenging task. The available methods can be classified broadly as site pattern frequency based and population genetic clustering approaches, though the performance of the two classes of methods under different hybridization scenarios has not been extensively examined. Here, we use simulated data to comparatively evaluate the performance of four tools that are commonly used to infer hybridization events: the site pattern frequency based methods HyDe and the D-statistic (i.e., the ABBA-BABA test), and the population clustering approaches structure and ADMIXTURE. We consider single hybridization scenarios that vary in the time of hybridization and the amount of incomplete lineage sorting (ILS) for different proportions of parental contributions (γ); introgressive hybridization; multiple hybridization scenarios; and a mixture of ancestral and recent hybridization scenarios. We focus on the statistical power to detect hybridization, the false discovery rate (FDR) for the D-statistic and HyDe, and the accuracy of the estimates of γ as measured by the mean squared error for HyDe, structure, and ADMIXTURE. Both HyDe and the D-statistic demonstrate a high level of detection power in all scenarios except those with high ILS, although the D-statistic often has an unacceptably high FDR. The estimates of γ in HyDe are impressively robust and accurate whereas structure and ADMIXTURE sometimes fail to identify hybrids, particularly when the proportional parental contributions are asymmetric (i.e., when γ is close to 0). Moreover, the posterior distribution estimated using structure exhibits multimodality in many scenarios, making interpretation difficult. Our results provide guidance in selecting appropriate methods for identifying hybrid populations from genomic data.

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
Keyword(s):  
Evolutionary Biology ◽  
De Novo ◽  
Phylogenetic Analyses ◽  
Introgressive Hybridization ◽  
Flower Colour ◽  
Adaptive Divergence ◽  
Evolutionary Mechanisms ◽  
Standing Variation ◽  
Regulatory Mutations ◽  
History Of

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.

scholarly journals Rapid phenotypic evolution during incipient speciation in a continental avian radiation

2011 ◽  
Vol 279 (1734) ◽  
pp. 1847-1856 ◽  
Author(s):  
Leonardo Campagna ◽  
Pilar Benites ◽  
Stephen C. Lougheed ◽  
Darío A. Lijtmaer ◽  
Adrián S. Di Giacomo ◽  
...  
Keyword(s):  
Phenotypic Diversity ◽  
Incomplete Lineage Sorting ◽  
Introgressive Hybridization ◽  
Molecular Data ◽  
Species Group ◽  
Adult Males ◽  
Lineage Sorting ◽  
Male Plumage ◽  
Recent Group ◽  
Genetic Signatures

Adaptive radiations have helped shape how we view animal speciation, particularly classic examples such as Darwin's finches, Hawaiian fruitflies and African Great Lakes cichlids. These ‘island’ radiations are comparatively recent, making them particularly interesting because the mechanisms that caused diversification are still in motion. Here, we identify a new case of a recent bird radiation within a continentally distributed species group; the capuchino seedeaters comprise 11 Sporophila species originally described on the basis of differences in plumage colour and pattern in adult males. We use molecular data together with analyses of male plumage and vocalizations to understand species limits of the group. We find marked phenotypic variation despite lack of mitochondrial DNA monophyly and few differences in other putatively neutral nuclear markers. This finding is consistent with the group having undergone a recent radiation beginning in the Pleistocene, leaving genetic signatures of incomplete lineage sorting, introgressive hybridization and demographic expansions. We argue that this apparent uncoupling between neutral DNA homogeneity and phenotypic diversity is expected for a recent group within the framework of coalescent theory. Finally, we discuss how the ecology of open habitats in South America during the Pleistocene could have helped promote this unique and ongoing radiation.

scholarly journals Plastomes of eight Ligusticum species: characterization, genome evolution, and phylogenetic relationships

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Ting Ren ◽  
Zi-Xuan Li ◽  
Deng-Feng Xie ◽  
Ling-Jian Gui ◽  
Chang Peng ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
De Novo ◽  
Incomplete Lineage Sorting ◽  
Phylogenetic Analyses ◽  
Morphological Characteristics ◽  
Purifying Selection ◽  
Repeat Sequence ◽  
Lineage Sorting ◽  
Plastome Evolution ◽  
Tree Topologies

Abstract Background The genus Ligusticum consists of approximately 60 species distributed in the Northern Hemisphere. It is one of the most taxonomically difficult taxa within Apiaceae, largely due to the varied morphological characteristics. To investigate the plastome evolution and phylogenetic relationships of Ligusticum, we determined the complete plastome sequences of eight Ligusticum species using a de novo assembly approach. Results Through a comprehensive comparative analysis, we found that the eight plastomes were similar in terms of repeat sequence, SSR, codon usage, and RNA editing site. However, compared with the other seven species, L. delavayi exhibited striking differences in genome size, gene number, IR/SC borders, and sequence identity. Most of the genes remained under the purifying selection, whereas four genes showed relaxed selection, namely ccsA, rpoA, ycf1, and ycf2. Non-monophyly of Ligusticum species was inferred from the plastomes and internal transcribed spacer (ITS) sequences phylogenetic analyses. Conclusion The plastome tree and ITS tree produced incongruent tree topologies, which may be attributed to the hybridization and incomplete lineage sorting. Our study highlighted the advantage of plastome with mass informative sites in resolving phylogenetic relationships. Moreover, combined with the previous studies, we considered that the current taxonomy system of Ligusticum needs to be improved and revised. In summary, our study provides new insights into the plastome evolution, phylogeny, and taxonomy of Ligusticum species.

Large-scale ruminant genome sequencing provides insights into their evolution and distinct traits

Science ◽  
2019 ◽  
Vol 364 (6446) ◽  
pp. eaav6202 ◽  
Author(s):  
Lei Chen ◽  
Qiang Qiu ◽  
Yu Jiang ◽  
Kun Wang ◽  
Zeshan Lin ◽  
...  
Keyword(s):  
Large Scale ◽  
De Novo ◽  
Incomplete Lineage Sorting ◽  
Regulatory Elements ◽  
Habitat Diversity ◽  
Human Populations ◽  
Population Declines ◽  
Lineage Sorting ◽  
Ruminant Species ◽  
System Metabolism

The ruminants are one of the most successful mammalian lineages, exhibiting morphological and habitat diversity and containing several key livestock species. To better understand their evolution, we generated and analyzed de novo assembled genomes of 44 ruminant species, representing all six Ruminantia families. We used these genomes to create a time-calibrated phylogeny to resolve topological controversies, overcoming the challenges of incomplete lineage sorting. Population dynamic analyses show that population declines commenced between 100,000 and 50,000 years ago, which is concomitant with expansion in human populations. We also reveal genes and regulatory elements that possibly contribute to the evolution of the digestive system, cranial appendages, immune system, metabolism, body size, cursorial locomotion, and dentition of the ruminants.

scholarly journals Diagnosis of the mechanisms of different types of discordances between phylogenies inferred from nuclear and mitochondrial markers

2020 ◽  
Vol 24 (4) ◽  
pp. 420-426
Author(s):  
A. A. Poroshina ◽  
D. Y. Sherbakov ◽  
T. E. Peretolchina
Keyword(s):  
Phylogenetic Trees ◽  
Environmental Changes ◽  
Incomplete Lineage Sorting ◽  
Adaptive Dynamics ◽  
Introgressive Hybridization ◽  
Sister Species ◽  
Complex Case ◽  
Special Focus ◽  
Large Species ◽  
Lineage Sorting

In ancient freshwater lakes, an abnormally large species diversity is observed. The mechanisms that g nerated extremely high biodiversity in the ancient lakes have not been sufficiently studied and remain only partially known. Sequences of environmental changes in highly complex ecosystems such as Lake Baikal, may induce sophisticated combinations of microevolutionary processes. These processes are likely to result in unusual “patterns” of genetic variability of species. The most unusual patterns include the ones when speciation is followed by incomplete lineage sorting as well as mitochondrial or nuclear introgression. All these phenomena are diagnosed by comparing the topologies of phylogenetic trees inferred from molecular markers of evolution located in mitochondria and nuclei. Mitochondrial and nuclear introgression is a particularly interesting and complex case, which is the process of incorporating the gene alleles of one species into the gene pool of a sister species due to interspecific hybridization (introgressive hybridization). In many cases, existing methods for molecular phylogenetic analysis do not automatically allow the observed patterns of polymorphism to be explained and, therefore, cannot provide hypotheses that would explain the mechanisms which resulted to these patterns. Here we use adaptive dynamics models to study neutral molecular evolution under various scenarios of interaction between sister species and the environment. We propose and justify a set of criteria for detecting how two evolutionary trees may differ, with a special focus on comparing a tree inferred from nuclear DNA to one from mitochondrial DNA. The criteria react to branching pattern and branch lengths, including relative distances from ancestral lineages. Simulations show that the criteria allow fast and automated detection of various types of introgression, secondary breaches of reproductive barriers, and incomplete lineage sorting.

scholarly journals Nepenthes × ventrata Transcriptome Profiling Reveals a Similarity Between the Evolutionary Origins of Carnivorous Traps and Floral Organs

2021 ◽  
Vol 12 ◽  
Author(s):  
Anna V. Shchennikova ◽  
Alexey V. Beletsky ◽  
Mikhail A. Filyushin ◽  
Maria A. Slugina ◽  
Eugeny V. Gruzdev ◽  
...  
Keyword(s):  
Evolutionary Biology ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
De Novo ◽  
Transcriptome Profiling ◽  
Mads Box ◽  
Mads Box Genes ◽  
Evolutionary Origins ◽  
Novel Structure ◽  
Genes Encoding

The emergence of the carnivory syndrome and traps in plants is one of the most intriguing questions in evolutionary biology. In the present study, we addressed it by comparative transcriptomics analysis of leaves and leaf-derived pitcher traps from a predatory plant Nepenthes ventricosa × Nepenthes alata. Pitchers were collected at three stages of development and a total of 12 transcriptomes were sequenced and assembled de novo. In comparison with leaves, pitchers at all developmental stages were found to be highly enriched with upregulated genes involved in stress response, specification of shoot apical meristem, biosynthesis of sucrose, wax/cutin, anthocyanins, and alkaloids, genes encoding digestive enzymes (proteases and oligosaccharide hydrolases), and flowering-related MADS-box genes. At the same time, photosynthesis-related genes in pitchers were transcriptionally downregulated. As the MADS-box genes are thought to be associated with the origin of flower organs from leaves, we suggest that Nepenthes species could have employed a similar pathway involving highly conserved MADS-domain transcription factors to develop a novel structure, pitcher-like trap, for capture and digestion of animal prey during the evolutionary transition to carnivory. The data obtained should clarify the molecular mechanisms of trap initiation and development and may contribute to solving the problem of its emergence in plants.

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