Reconstructing the past

2019 ◽  
pp. 214-249
Author(s):  
Glenn-Peter Sætre ◽  
Mark Ravinet

How can genetics and genomics be used to understand the evolutionary history of organisms? This chapter focuses on such methods. First, the field of phylogenetics is introduced, as a way to visualize and quantify the evolutionary relationships among species. The chapter outlines how we go from aligning DNA sequence data to building gene trees and we argue that “tree-thinking” is fundamentally important for understanding evolution. The chapter also goes beyond phylogenetic trees to focus on phylogeography, i.e. the understanding of evolutionary relationships in a spatial context. More recently, the explosion of genomic data from ancient and modern human populations has made this an extremely exciting field which is transforming our understanding of our own evolutionary history. Before that, though, the chapter reviews how modern phylogenetics has arisen from historical efforts to classify life on Earth.

2006 ◽  
Vol 04 (01) ◽  
pp. 59-74 ◽  
Author(s):  
YING-JUN HE ◽  
TRINH N. D. HUYNH ◽  
JESPER JANSSON ◽  
WING-KIN SUNG

To construct a phylogenetic tree or phylogenetic network for describing the evolutionary history of a set of species is a well-studied problem in computational biology. One previously proposed method to infer a phylogenetic tree/network for a large set of species is by merging a collection of known smaller phylogenetic trees on overlapping sets of species so that no (or as little as possible) branching information is lost. However, little work has been done so far on inferring a phylogenetic tree/network from a specified set of trees when in addition, certain evolutionary relationships among the species are known to be highly unlikely. In this paper, we consider the problem of constructing a phylogenetic tree/network which is consistent with all of the rooted triplets in a given set [Formula: see text] and none of the rooted triplets in another given set [Formula: see text]. Although NP-hard in the general case, we provide some efficient exact and approximation algorithms for a number of biologically meaningful variants of the problem.


2005 ◽  
Vol 18 (1) ◽  
pp. 41 ◽  
Author(s):  
L. A. Orthia ◽  
L. G. Cook ◽  
M. D. Crisp

Phylogenetic trees can provide a stable basis for a higher-level classification of organisms that reflects evolutionary relationships. However, some lineages have a complex evolutionary history that involves explosive radiation or hybridisation. Such histories have become increasingly apparent with the use of DNA sequence data for phylogeny estimation and explain, in part, past difficulties in producing stable morphology-based classifications for some groups. We illustrate this situation by using the example of tribe Mirbelieae (Fabaceae), whose generic classification has been fraught for decades. In particular, we discuss a recent proposal to combine 19 of the 25 Mirbelieae genera into a single genus, Pultenaea sens. lat., and how we might find stable and consistent ways to squeeze something as complex as life into little boxes for our own convenience.


2006 ◽  
Vol 17 (3) ◽  
Author(s):  
Andreas Düring ◽  
Martina Brückner ◽  
Dietrich Mossakowski

Phylogenetic analyses of Chrysocarabus taxa using different markers result in different phylogenetic trees. In particular, the mitochondrial gene tree contradicts the results of morphological and inbreeding studies. Two very different haplotypes of Carabus splendens Olivier, 1790 do not form a clade within this phylogenetic tree. We have earlier proposed that contradictory results are due to introgression. To verify our hypothesis, we analysed the internal transcribed spacer 2. No substitutions were observed in these nuclear sequences between the individuals of Carabus splendens, which contain the different mitochondrial haplotypes in question. The differences in the gene trees based on mitochondrial and nuclear sequences can be explained with at least two introgression events.


2016 ◽  
Vol 16 (1) ◽  
pp. 40-59 ◽  
Author(s):  
Claudio Maccone

AbstractIn two recent papers (Maccone 2013, 2014) as well as in the book (Maccone 2012), this author described the Evolution of life on Earth over the last 3.5 billion years as a lognormal stochastic process in the increasing number of living Species. In (Maccone 2012, 2013), the process used was ‘Geometric Brownian Motion’ (GBM), largely used in Financial Mathematics (Black-Sholes models). The GBM mean value, also called ‘the trend’, always is an exponential in time and this fact corresponds to the so-called ‘Malthusian growth’ typical of population genetics. In (Maccone 2014), the author made an important generalization of his theory by extending it to lognormal stochastic processes having an arbitrary trend mL(t), rather than just a simple exponential trend as the GBM have.The author named ‘Evo-SETI’ (Evolution and SETI) his theory inasmuch as it may be used not only to describe the full evolution of life on Earth from RNA to modern human societies, but also the possible evolution of life on exoplanets, thus leading to SETI, the current Search for ExtraTerrestrial Intelligence. In the Evo-SETI Theory, the life of a living being (let it be a cell or an animal or a human or a Civilization of humans or even an ET Civilization) is represented by a b-lognormal, i.e. a lognormal probability density function starting at a precise instant b (‘birth’) then increasing up to a peak-time p, then decreasing to a senility-time s (the descending inflexion point) and then continuing as a straight line down to the death-time d (‘finite b-lognormal’).(1)Having so said, the present paper describes the further mathematical advances made by this author in 2014–2015, and is divided in two halves: Part One, devoted to new mathematical results about the History of Civilizations as b-lognormals, and(2)Part Two, about the applications of the Evo-SETI Theory to the Molecular Clock, well known to evolutionary geneticists since 50 years: the idea is that our EvoEntropy grows linearly in time just as the molecular clock. (a)Summarizing the new results contained in this paper: In Part One, we start from the History Formulae already given in (Maccone 2012, 2013) and improve them by showing that it is possible to determine the b-lognormal not only by assigning its birth, senility and death, but rather by assigning birth, peak and death (BPD Theorem: no assigned senility). This is precisely what usually happens in History, when the life of a VIP is summarized by giving birth time, death time, and the date of the peak of activity in between them, from which the senility may then be calculated (approximately only, not exactly). One might even conceive a b-scalene (triangle) probability density just centred on these three points (b, p, d) and we derive the relevant equations. As for the uniform distribution between birth and death only, that is clearly the minimal description of someone's life, we compare it with both the b-lognormal and the b-scalene by comparing the Shannon Entropy of each, which is the measure of how much information each of them conveys. Finally we prove that the Central Limit Theorem (CLT) of Statistics becomes a new ‘E-Pluribus-Unum’ Theorem of the Evo-SETI Theory, giving formulae by which it is possible to find the b-lognormal of the History of a Civilization C if the lives of its Citizens Ci are known, even if only in the form of birth and death for the vast majority of the Citizens.(b)In Part Two, we firstly prove the crucial Peak-Locus Theorem for any given trend mL(t) and not just for the GBM exponential. Then we show that the resulting Evo-Entropy grows exactly linearly in time if the trend is the exponential GMB trend.(c)In addition, three Appendixes (online) with all the relevant mathematical proofs are attached to this paper. They are written in the Maxima language, and Maxima is a symbolic manipulator that may be downloaded for free from the web.In conclusion, this paper further increases the huge mathematical spectrum of applications of the Evo-SETI Theory to prepare Humans for the first Contact with an Extra-Terrestrial Civilization.


2010 ◽  
Vol 19 (R2) ◽  
pp. R197-R203 ◽  
Author(s):  
T. Lappalainen ◽  
E. T. Dermitzakis

2019 ◽  
Vol 11 (9) ◽  
pp. 2531-2541 ◽  
Author(s):  
Valeria Mateo-Estrada ◽  
Lucía Graña-Miraglia ◽  
Gamaliel López-Leal ◽  
Santiago Castillo-Ramírez

Abstract The Gram-negative Acinetobacter genus has several species of clear medical relevance. Many fully sequenced genomes belonging to the genus have been published in recent years; however, there has not been a recent attempt to infer the evolutionary history of Acinetobacter with that vast amount of information. Here, through a phylogenomic approach, we established the most up-to-date view of the evolutionary relationships within this genus and highlighted several cases of poor classification, especially for the very closely related species within the Acinetobacter calcoaceticus–Acinetobacter baumannii complex (Acb complex). Furthermore, we determined appropriate phylogenetic markers for this genus and showed that concatenation of the top 13 gives a very decent reflection of the evolutionary relationships for the genus Acinetobacter. The intersection between our top markers and previously defined universal markers is very small. In general, our study shows that, although there seems to be hardly any universal markers, bespoke phylogenomic approaches can be used to infer the phylogeny of different bacterial genera. We expect that ad hoc phylogenomic approaches will be the standard in the years to come and will provide enough information to resolve intricate evolutionary relationships like those observed in the Acb complex.


Data in Brief ◽  
2018 ◽  
Vol 18 ◽  
pp. 1972-1975 ◽  
Author(s):  
Shaoyuan Wu ◽  
Scott Edwards ◽  
Liang Liu

2006 ◽  
Vol 273 (1598) ◽  
pp. 2119-2125 ◽  
Author(s):  
Ross Barnett ◽  
Nobuyuki Yamaguchi ◽  
Ian Barnes ◽  
Alan Cooper

Understanding the phylogeographic processes affecting endangered species is crucial both to interpreting their evolutionary history and to the establishment of conservation strategies. Lions provide a key opportunity to explore such processes; however, a lack of genetic diversity and shortage of suitable samples has until now hindered such investigation. We used mitochondrial control region DNA (mtDNA) sequences to investigate the phylogeographic history of modern lions, using samples from across their entire range. We find the sub-Saharan African lions are basal among modern lions, supporting a single African origin model of modern lion evolution, equivalent to the ‘recent African origin’ model of modern human evolution. We also find the greatest variety of mtDNA haplotypes in the centre of Africa, which may be due to the distribution of physical barriers and continental-scale habitat changes caused by Pleistocene glacial oscillations. Our results suggest that the modern lion may currently consist of three geographic populations on the basis of their recent evolutionary history: North African–Asian, southern African and middle African. Future conservation strategies should take these evolutionary subdivisions into consideration.


2011 ◽  
Vol 09 (06) ◽  
pp. 729-747 ◽  
Author(s):  
MD. SHAIK SADI ◽  
FEI-CHING KUO ◽  
JOSHUA W. K. HO ◽  
MICHAEL A. CHARLESTON ◽  
T. Y. CHEN

Many phylogenetic inference programs are available to infer evolutionary relationships among taxa using aligned sequences of characters, typically DNA or amino acids. These programs are often used to infer the evolutionary history of species. However, in most cases it is impossible to systematically verify the correctness of the tree returned by these programs, as the correct evolutionary history is generally unknown and unknowable. In addition, it is nearly impossible to verify whether any non-trivial tree is correct in accordance to the specification of the often complicated search and scoring algorithms. This difficulty is known as the oracle problem of software testing: there is no oracle that we can use to verify the correctness of the returned tree. This makes it very challenging to test the correctness of any phylogenetic inference programs. Here, we demonstrate how to apply a simple software testing technique, called Metamorphic Testing, to alleviate the oracle problem in testing phylogenetic inference programs. We have used both real and randomly generated test inputs to evaluate the effectiveness of metamorphic testing, and found that metamorphic testing can detect failures effectively in faulty phylogenetic inference programs with both types of test inputs.


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