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 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 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 Incomplete Lineage Sorting and Hybridization Statistics for Large-Scale Retroposon Insertion Data

2016 ◽  
Vol 12 (3) ◽  
pp. e1004812 ◽  
Author(s):  
Andrej Kuritzin ◽  
Tabea Kischka ◽  
Jürgen Schmitz ◽  
Gennady Churakov
Keyword(s):  
Large Scale ◽  
Incomplete Lineage Sorting ◽  
Lineage Sorting

scholarly journals Alu insertion polymorphisms shared by Papio baboons and Theropithecus gelada reveal an intertwined common ancestry

Mobile DNA ◽  
2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Jerilyn A. Walker ◽  
◽  
Vallmer E. Jordan ◽  
Jessica M. Storer ◽  
Cody J. Steely ◽  
...  
Keyword(s):  
Large Scale ◽  
Incomplete Lineage Sorting ◽  
Genetic Relationships ◽  
Whole Genome Sequence ◽  
Lineage Sorting ◽  
High Coverage ◽  
Theropithecus Gelada ◽  
Alu Insertion ◽  
Genomic Markers ◽  
Additional Support

Abstract Background Baboons (genus Papio) and geladas (Theropithecus gelada) are now generally recognized as close phylogenetic relatives, though morphologically quite distinct and generally classified in separate genera. Primate specific Alu retrotransposons are well-established genomic markers for the study of phylogenetic and population genetic relationships. We previously reported a computational reconstruction of Papio phylogeny using large-scale whole genome sequence (WGS) analysis of Alu insertion polymorphisms. Recently, high coverage WGS was generated for Theropithecus gelada. The objective of this study was to apply the high-throughput “poly-Detect” method to computationally determine the number of Alu insertion polymorphisms shared by T. gelada and Papio, and vice versa, by each individual Papio species and T. gelada. Secondly, we performed locus-specific polymerase chain reaction (PCR) assays on a diverse DNA panel to complement the computational data. Results We identified 27,700 Alu insertions from T. gelada WGS that were also present among six Papio species, with nearly half (12,956) remaining unfixed among 12 Papio individuals. Similarly, each of the six Papio species had species-indicative Alu insertions that were also present in T. gelada. In general, P. kindae shared more insertion polymorphisms with T. gelada than did any of the other five Papio species. PCR-based genotype data provided additional support for the computational findings. Conclusions Our discovery that several thousand Alu insertion polymorphisms are shared by T. gelada and Papio baboons suggests a much more permeable reproductive barrier between the two genera then previously suspected. Their intertwined evolution likely involves a long history of admixture, gene flow and incomplete lineage sorting.

scholarly journals Phylogeny and Species Delimitation of Chinese Medicago (Leguminosae) and Its Relatives Based on Molecular and Morphological Evidence

2021 ◽  
Vol 11 ◽  
Author(s):  
Jinyuan Chen ◽  
Guili Wu ◽  
Nawal Shrestha ◽  
Shuang Wu ◽  
Wei Guo ◽  
...  
Keyword(s):  
Phylogenetic Relationship ◽  
Species Delimitation ◽  
Large Scale ◽  
Incomplete Lineage Sorting ◽  
Phylogenetic Analyses ◽  
Population Based ◽  
Integrative Approach ◽  
Morphological Evidence ◽  
Sampling Errors ◽  
Lineage Sorting

Medicago and its relatives, Trigonella and Melilotus comprise the most important forage resources globally. The alfalfa selected from the wild relatives has been cultivated worldwide as the forage queen. In the Flora of China, 15 Medicago, eight Trigonella, and four Melilotus species are recorded, of which six Medicago and two Trigonella species are introduced. Although several studies have been conducted to investigate the phylogenetic relationship within the three genera, many Chinese naturally distributed or endemic species are not included in those studies. Therefore, the taxonomic identity and phylogenetic relationship of these species remains unclear. In this study, we collected samples representing 18 out of 19 Chinese naturally distributed species of these three genera and three introduced Medicago species, and applied an integrative approach by combining evidences from population-based morphological clusters and molecular data to investigate species boundaries. A total of 186 individuals selected from 156 populations and 454 individuals from 124 populations were collected for genetic and morphological analyses, respectively. We sequenced three commonly used DNA barcodes (trnH-psbA, trnK-matK, and ITS) and one nuclear marker (GA3ox1) for phylogenetic analyses. We found that 16 out of 21 species could be well delimited based on phylogenetic analyses and morphological clusters. Two Trigonella species may be merged as one species or treated as two subspecies, and Medicago falcata should be treated as a subspecies of the M. sativa complex. We further found that major incongruences between the chloroplast and nuclear trees mainly occurred among the deep diverging lineages, which may be resulted from hybridization, incomplete lineage sorting and/or sampling errors. Further studies involving a finer sampling of species associated with large scale genomic data should be employed to better understand the species delimitation of these three genera.

scholarly journals A Divide-and-Conquer Method for Scalable Phylogenetic Network Inference from Multi-locus Data

2019 ◽  
Author(s):  
Jiafan Zhu ◽  
Xinhao Liu ◽  
Huw A. Ogilvie ◽  
Luay K. Nakhleh
Keyword(s):  
Large Scale ◽  
Network Inference ◽  
Incomplete Lineage Sorting ◽  
Phylogenetic Network ◽  
Biological Data ◽  
Phylogenetic Networks ◽  
Divide And Conquer ◽  
Lineage Sorting ◽  
Step Method ◽  
Sequence Alignments

AbstractReticulate evolutionary histories, such as those arising in the presence of hybridization, are best modeled as phylogenetic networks. Recently developed methods allow for statistical inference of phylogenetic networks while also accounting for other processes, such as incomplete lineage sorting (ILS). However, these methods can only handle a small number of loci from a handful of genomes.In this paper, we introduce a novel two-step method for scalable inference of phylogenetic networks from the sequence alignments of multiple, unlinked loci. The method infers networks on subproblems and then merges them into a network on the full set of taxa. To reduce the number of trinets to infer, we formulate a Hitting Set version of the problem of finding a small number of subsets, and implement a simple heuristic to solve it. We studied their performance, in terms of both running time and accuracy, on simulated as well as on biological data sets. The two-step method accurately infers phylogenetic networks at a scale that is infeasible with existing methods. The results are a significant and promising step towards accurate, large-scale phylogenetic network inference.We implemented the algorithms in the publicly available software package PhyloNet (https://bioinfocs.rice.edu/PhyloNet)[email protected]

scholarly journals Genomic insights into adaptive divergence and speciation among malaria vectors of the Anopheles nili group

2016 ◽  
Author(s):  
Caroline Fouet ◽  
Colince Kamdem ◽  
Stephanie Gamez ◽  
Bradley J. White
Keyword(s):  
Population Structure ◽  
Large Scale ◽  
Incomplete Lineage Sorting ◽  
Snp Markers ◽  
Malaria Vectors ◽  
Adaptive Divergence ◽  
Nucleotide Polymorphisms ◽  
Lineage Sorting ◽  
Interspecific Gene Flow ◽  
Scale Control

AbstractOngoing speciation in most African malaria vectors gives rise to cryptic populations, which differ remarkably in their behaviour, ecology and capacity to vector malaria parasites. Understanding the population structure and the drivers of genetic differentiation among mosquitoes is critical for effective disease control because heterogeneity within species contribute to variability in malaria cases and allow fractions of vector populations to escape control efforts. To examine the population structure and the potential impacts of recent large-scale control interventions, we have investigated the genomic patterns of differentiation in mosquitoes belonging to the Anopheles nili group, a large taxonomic group that diverged ∼3-Myr ago. Using 4343 single nucleotide polymorphisms (SNPs), we detected strong population structure characterized by high FST values between multiple divergent populations adapted to different habitats within the Central African rainforest. Delineating the cryptic species within the Anopheles nili group is challenging due to incongruence between morphology, ribosomal DNA and SNP markers consistent with incomplete lineage sorting and/or interspecific gene flow. A very high proportion of loci are fixed (FST = 1) within the genome of putative species, which suggests that ecological and/or reproductive barriers are maintained by strong selection on a substantial number of genes.

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.

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