Computational approaches to species phylogeny inference and gene tree reconciliation

Nakhleh, Luay

doi:10.1016/j.tree.2013.09.004

Cited by 196 publications

(136 citation statements)

References 96 publications

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“…In particular, diversity of the nuclear genome is unlikely to be reciprocally monophyletic among subpopulations, a phenomenon called incomplete lineage sorting, which results in support for different topologies across loci (27). We therefore used several approaches and different nuclear markers to infer the phylogenetic relationships and to estimate the amount of gene flow between ancient and modern horses.…”

Section: Resultsmentioning

confidence: 99%

Prehistoric genomes reveal the genetic foundation and cost of horse domestication

Schubert

Jónsson

Chang

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

272

281

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The domestication of the horse ∼5.5 kya and the emergence of mounted riding, chariotry, and cavalry dramatically transformed human civilization. However, the genetics underlying horse domestication are difficult to reconstruct, given the near extinction of wild horses. We therefore sequenced two ancient horse genomes from Taymyr, Russia (at 7.4-and 24.3-fold coverage), both predating the earliest archeological evidence of domestication. We compared these genomes with genomes of domesticated horses and the wild Przewalski's horse and found genetic structure within Eurasia in the Late Pleistocene, with the ancient population contributing significantly to the genetic variation of domesticated breeds. We furthermore identified a conservative set of 125 potential domestication targets using four complementary scans for genes that have undergone positive selection. One group of genes is involved in muscular and limb development, articular junctions, and the cardiac system, and may represent physiological adaptations to human utilization. A second group consists of genes with cognitive functions, including social behavior, learning capabilities, fear response, and agreeableness, which may have been key for taming horses. We also found that domestication is associated with inbreeding and an excess of deleterious mutations. This genetic load is in line with the "cost of domestication" hypothesis also reported for rice, tomatoes, and dogs, and it is generally attributed to the relaxation of purifying selection resulting from the strong demographic bottlenecks accompanying domestication. Our work demonstrates the power of ancient genomes to reconstruct the complex genetic changes that transformed wild animals into their domesticated forms, and the population context in which this process took place.ancient DNA | horse domestication | Przewalski's horse | positive selection | cost of domestication T he domestication of the horse had a far-reaching impact on the sociopolitical and economic trajectories of human societies (1). It not only provided meat and milk (2) but also enabled the development of continent-sized nomadic empires, by transforming warfare and allowing for the rapid spread of goods and information over long distances. However, despite the characterization of the genome of modern horses (3), an understanding of the genetic processes underlying horse domestication is still lacking. In other organisms, such an understanding is usually achieved by comparing the genomes of domesticated species and their wild relatives (4-6), but this approach is not directly applicable to horses. Recent genome-wide analyses have shown that Przewalski's horse, the last truly wild horse population remaining today, is not the direct ancestor of domesticated SignificanceThe domestication of the horse revolutionized warfare, trade, and the exchange of people and ideas. This at least 5,500-ylong process, which ultimately transformed wild horses into the hundreds of breeds living today, is difficult to reconstruct from archeological data...

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Section: Resultsmentioning

confidence: 99%

Prehistoric genomes reveal the genetic foundation and cost of horse domestication

Schubert

Jónsson

Chang

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

272

281

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“…Narechania et al (2012) defined core genome as orthologs with the same phylogenetic tree topology and the shell genome as composed of the rest of orthologs. Core genes may also exhibit evidence of HGT events, which might be identified by comparing scenarios of gene phylogenies with individual species trees Nakhleh 2013). The question remains, though, do these changes provide enough force to diverge evolutionary lineages with subsequent cohesion to form an analogue of the eukaryotic ''sexual'' species?…”

Section: Speciation Factors In (Cyano)bacteriamentioning

confidence: 99%

Species concepts and speciation factors in cyanobacteria, with connection to the problems of diversity and classification

et al. 2015

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The cyanobacteria are the most important prokaryotic primary producers on Earth, inhabiting a great diversity of aquatic and terrestrial environments exposed to light. However, the evolutionary forces leading to their divergence and speciation remain largely enigmatic compared to macroorganisms due to their prokaryotic nature, including vast population sizes, and largely asexual reproduction. The advent of modern molecular techniques has facilitated an understanding of the important factors shaping cyanobacterial evolution, including horizontal gene transfer and homologous recombination. We review the forces shaping the evolution of cyanobacteria and discuss the role of cohesive forces on speciation. Further, while myriad species concepts and definitions are currently used, only a limited subset might be applied to cyanobacteria due to their asexual reproduction. Additionally, concepts based solely on phenotypes provide insufficient resolution. A monophyletic species concept which is universal may be ideal for cyanobacteria. Actual identification of the cyanobacteria is difficult due to cryptic diversity, lack of morphological variability, and frequent convergent evolutionary events. Thus, applied molecular techniques such as DNA barcoding will be useful for identifications of environmental samples. Lastly, we show that the real biodiversity of the cyanobacteria is widely underestimated, due in part to low sampling efforts, sensitivity to the molecular markers 123Biodivers Conserv (2015) 24:739-757 DOI 10.1007 employed, and the species definitions employed by researchers. In conclusion, we anticipate a rapid increase in cyanobacterial taxa described and large revisions of the system in the future as scientists adopt a common approach to cyanobacterial systematics.

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“…In reality, however, one has to estimate gene trees and coalescent times from finite, say, length-k molecular sequences. Taking into account the resulting estimation errors at the gene level is key to mathematically quantify and compare the performance of different methods (see e.g., [13], [14], [15]). Intuitively, for instance, the "minimum" used in GLASS may be significantly more sensitive to estimation errors than the "average" used in STEAC.…”

Section: Arxiv:14047055v2 [Q-biope] 30 Jun 2014mentioning

confidence: 99%

Data Requirement for Phylogenetic Inference from Multiple Loci: A New Distance Method

Dasarathy

Nowak

Roch

2015

IEEE/ACM Trans. Comput. Biol. and Bioinf.

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We consider the problem of estimating the evolutionary history of a set of species (phylogeny or species tree) from several genes. It is known that the evolutionary history of individual genes (gene trees) might be topologically distinct from each other and from the underlying species tree, possibly confounding phylogenetic analysis. A further complication in practice is that one has to estimate gene trees from molecular sequences of finite length. We provide the first full data-requirement analysis of a species tree reconstruction method that takes into account estimation errors at the gene level. Under that criterion, we also devise a novel reconstruction algorithm that provably improves over all previous methods in a regime of interest.

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Computational approaches to species phylogeny inference and gene tree reconciliation

Cited by 196 publications

References 96 publications

Prehistoric genomes reveal the genetic foundation and cost of horse domestication

Prehistoric genomes reveal the genetic foundation and cost of horse domestication

Species concepts and speciation factors in cyanobacteria, with connection to the problems of diversity and classification

Data Requirement for Phylogenetic Inference from Multiple Loci: A New Distance Method

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