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1.
T. Ryan Gregory 《Evolution》2008,1(2):121-137
Charles Darwin sketched his first evolutionary tree in 1837, and trees have remained a central metaphor in evolutionary biology
up to the present. Today, phylogenetics—the science of constructing and evaluating hypotheses about historical patterns of
descent in the form of evolutionary trees—has become pervasive within and increasingly outside evolutionary biology. Fostering
skills in “tree thinking” is therefore a critical component of biological education. Conversely, misconceptions about evolutionary
trees can be very detrimental to one’s understanding of the patterns and processes that have occurred in the history of life.
This paper provides a basic introduction to evolutionary trees, including some guidelines for how and how not to read them.
Ten of the most common misconceptions about evolutionary trees and their implications for understanding evolution are addressed.
相似文献
T. Ryan GregoryEmail: |
2.
Today, the picture of an evolutionary tree is a very well-known visual image. It is almost impossible to think of the ancestry
and relationships of living beings without it. As natural history museums play a major role in the public understanding of
evolution, they often present a wide variety of evolutionary trees. However, many studies have shown (Baum and Offner 2008; Baum et al. 2005; Catley and Novick 2008; Evans 2009; Gregory 2008; Matuk 2007; Meir et al. 2007b; Padian 2008) that even though evolutionary trees have the potential to engage visitors of natural history museums with the phenomena
of evolution, many of them unwittingly might lead to misunderstandings about the process. As valuable research and educational
institutions, one of the museum’s important missions should be the careful design of their exhibits on evolution considering,
for example, common preconceptions visitors often bring, such as the notion that evolution is oriented from simple toward
complex organisms (incarnating the idea of a single ladder of life amidst the extraordinary diversity of organisms) and that
humans are at the pinnacle of the evolutionary story, as well as na?ve interpretations of phylogenies. Our aim in this article
is to show from history where many of these misunderstandings come from and to determine whether five important Western natural
history museums inadvertently present “problematic” evolutionary trees (which might lead to non-scientific notions). 相似文献
3.
Cladograms, phylogenetic trees that depict evolutionary relationships among a set of taxa, are one of the most powerful predictive
tools in modern biology. They are usually depicted in one of two formats—tree or ladder. Previous research (Novick and Catley
2007) has found that college students have much greater difficulty understanding a cladogram’s hierarchical structure when it
is depicted in the ladder format. Such understanding would seem to be a prerequisite for successful tree thinking. The present
research examined the effect of a theoretically guided manipulation—adding a synapomorphy on each branch that supports two
or more taxa—on students’ understanding of the hierarchical structure of ladder cladograms. Synapomorphies are characters
shared by a group of taxa due to inheritance from a common ancestor. Thus, their depiction on a cladogram may facilitate the
understanding of evolutionary relationships. Students’ comprehension was assessed in terms of success at translating relationships
depicted in the ladder format to the tree format. The results indicated that adding synapomorphies provided powerful conceptual
scaffolding that improved comprehension for students with both weaker and stronger backgrounds in biology. For stronger background
students, the benefit of adding synapomorphies to the ladders was comparable to that of approximately two hours of instruction
in phylogenetics that emphasized the ladder format. 相似文献
4.
Eric A. Gaucher James T. Kratzer Ryan N. Randall 《Cold Spring Harbor perspectives in biology》2010,2(1)
The Darwinian concept of biological evolution assumes that life on Earth shares a common ancestor. The diversification of this common ancestor through speciation events and vertical transmission of genetic material implies that the classification of life can be illustrated in a tree-like manner, commonly referred to as the Tree of Life. This article describes features of the Tree of Life, such as how the tree has been both pruned and become bushier throughout the past century as our knowledge of biology has expanded. We present current views that the classification of life may be best illustrated as a ring or even a coral with tree-like characteristics. This article also discusses how the organization of the Tree of Life offers clues about ancient life on Earth. In particular, we focus on the environmental conditions and temperature history of Precambrian life and show how chemical, biological, and geological data can converge to better understand this history.
“You know, a tree is a tree. How many more do you need to look at?”–Ronald Reagan (Governor of California), quoted in the Sacramento Bee, opposing expansion of Redwood National Park, March 3, 1966The following article addresses a period in life most removed from life’s origins compared with other articles in this collection. The article discusses an advanced form of life that seems to have lived on the order of 3.5–4.0 billion years ago, around the time when life as we know it began to diversify in a Darwinian sense. The life from this geological period is located deep within an illustrated taxonomic tree of life. The hope is that by understanding how early life evolved, we can better understand how life originated. In this sense, the article attempts to travel backwards in time, starting from modern organisms, to understand life’s origin.The Darwinian concept of evolution suggests that all modern life shares a single common ancestor, often referred to as the last universal common ancestor (LUCA). Throughout evolutionary history, this ancestor has for the most part generated descendants as successive bifurcations in a tree-like manner. This so called Tree of Life, and phylogenetics in general provides much of the framework for the field of molecular evolution. Taxonomic trees allow us to better understand relationships and commonalities shared by life. For instance, a tree may tell us whether a trait or phenotype shared between two organisms is the result of shared-common ancestry (termed homologous traits) or whether the trait has evolved multiple times independent of ancestry (analogous traits such as wings).Taxonomic trees can be built using diverse sources of information. These can include morphological and phenotypic data at the macro-level down to DNA and protein sequence data at the micro-level. Ideally, trees built from multiple sources of input have identical taxonomic relationships and branching patterns, and such trees are said to be congruent. In practice, however, trees built from morphological data (say, presence or absence of wings) are often different than a tree built from molecular data (DNA or protein sequences). This requires the biologist to determine which of the two data sets is misleading and/or which taxonomic tree-building algorithm is most appropriate to use for a particular data set. Such an artform is common in the field of molecular evolution because rarely are trees congruent when built from two sources of input data.In light of this fact, we have provided the quote at the beginning of this article as a reflection about the field of molecular evolution and its interpretations of taxonomic trees. Although Reagan was not speaking about taxonomic trees in his quote, the same sort of disconnect exists between evolutionary biologists and molecular biologists (Woese and Goldenfeld 2009), as it did between conservationists and Ronald Reagan. A molecular biologist may be inclined to say that once you have seen one phylogenetic tree, you have seen them all. And in fairness, there is some validity to such a notion because historically a phylogenetic tree could not help a molecular biologist to better describe their system. An evolutionary biologist, however, will argue that individual trees have nuances that can dramatically alter our interpretation of evolutionary processes.We intend to show in this article that not all (taxonomic) trees look similar and describe identical evolutionary scenarios. We will discuss how our concept of the Tree of Life has changed over the past couple of decades, how trees can be interpreted, and what a tree can tell us about early life. In particular, the article will focus on the temperature conditions of early life because this topic has received much attention over the past few years as a direct result of improved DNA sequencing technology and a better understanding of molecular evolutionary processes. We will also describe how trees can be used to guide laboratory experiments in our attempt to understand ancient life. Lastly, we will discuss how phylogenetic trees will serve as the foundation for an “evolutionary synthetic biology” that should allow us to better understand the evolution of cellular pathways, macromolecular machines such as the ribosome, and other emergent properties of early life. 相似文献
5.
Joel D. Velasco 《Biology & philosophy》2008,23(4):455-473
Bayesian methods have become among the most popular methods in phylogenetics, but theoretical opposition to this methodology
remains. After providing an introduction to Bayesian theory in this context, I attempt to tackle the problem mentioned most
often in the literature: the “problem of the priors”—how to assign prior probabilities to tree hypotheses. I first argue that
a recent objection—that an appropriate assignment of priors is impossible—is based on a misunderstanding of what ignorance
and bias are. I then consider different methods of assigning prior probabilities to trees. I argue that priors need to be
derived from an understanding of how distinct taxa have evolved and that the appropriate evolutionary model is captured by
the Yule birth–death process. This process leads to a well-known statistical distribution over trees. Though further modifications
may be necessary to model more complex aspects of the branching process, they must be modifications to parameters in an underlying
Yule model. Ignoring these Yule priors commits a fallacy leading to mistaken inferences both about the trees themselves and
about macroevolutionary processes more generally. 相似文献
6.
The 55-million-year fossil record of horses (Family Equidae) has been frequently cited as a prime example of long-term macroevolution.
In the second half of the nineteenth century, natural history museum exhibits characteristically depicted fossil horses to
be a single, straight-line (orthogenetic) progression from ancestor to descendent. By the beginning of the twentieth century,
however, paleontologists realized that, rather than representing orthogenesis, the evolutionary pattern of fossil horses was
more correctly characterized by a complexly branching phylogenetic tree. We conducted a systematic survey of 20 fossil horse
exhibits from natural history museums in the United States. Our resulting data indicate that more than half (55%) of natural
history museums today still depict horse evolution as orthogenetic, despite the fact that paleontologists have known for a
century that the actual evolutionary pattern of the Family Equidae is branching. Depicting outmoded evolutionary patterns
and concepts via museum exhibits, such as fossils horses exemplifying orthogenesis, not only communicates outmoded knowledge
but also likely contributes to general misconceptions about evolution for natural history museum visitors. 相似文献
7.
Kieran P. McNulty 《Evolution》2010,3(3):322-332
The evolutionary history of humans comprises an important but small branch on the larger tree of ape evolution. Today’s hominoids—gibbons,
orangutans, gorillas, chimpanzees, and humans—are a meager representation of the ape diversity that characterized the Old
World from 23–5 million years ago. In this paper, I briefly review this evolutionary history focusing on features important
for understanding modern ape and human origins. As the full complexity of ape evolution is beyond this review, I characterize
major geographic, temporal, and phylogenetic groups using a few flagship taxa. Improving our knowledge of hominoid evolution
both complicates and clarifies studies of human origins. On one hand, features thought to be unique to the human lineage find
parallels in some fossil ape species, reducing their usefulness for identifying fossil humans. On the other hand, the Miocene
record of fossil apes provides an important source for generating hypotheses about the ancestral human condition; this is
particularly true given the dearth of fossils representing our closest living relatives: chimpanzees and gorillas. 相似文献
8.
Museums play a vitally important role in supporting both informal and formal education and are important venues for fostering
public understanding of evolution. The Yale Peabody Museum has implemented significant education programs on evolution for
many decades, mostly focused on the museum’s extensive collections that represent the past and present tree of life. Twelve
years ago, the Peabody began a series of new programs that explored biodiversity and evolution as it relates to human health.
Modern evolutionary theory contributes significantly to our understanding of health and disease, and medical topics provide
many excellent and relevant examples to explore evolutionary concepts. The Peabody developed a program on vector-borne diseases,
specifically Lyme disease and West Nile virus, which have become endemic in the United States. Both of these diseases have
complex transmission cycles involving an intricate interplay among the pathogen, host, and vector, each of which is subject
to differing evolutionary pressures. Using these stories, the museum explored evolutionary concepts of adaptation (e.g., the
evolution of blood feeding), coevolution (e.g., the “arms race” between host and vector), and variation and selection (e.g.,
antibiotic resistance) among others. The project included a temporary exhibition and the development of curriculum materials
for middle and high school teachers and students. The popularity of the exhibit and some formal evaluation of student participants
suggested that this educational approach has significant potential to engage wide audiences in evolutionary issues. In addition
it demonstrated how natural history museums can incorporate evolution into a broad array of programs. 相似文献
9.
Three museum professionals with extensive expertise in informal science education about evolution—Warren D. Allmon, Judy Diamond,
and Martin Weiss—are interviewed about the interaction of teachers and natural history museums and science centers in improving
the effectiveness of evolution education. 相似文献
10.
T. Ryan Gregory 《Evolution》2008,1(3):259-273
The occurrence, generality, and causes of large-scale evolutionary trends—directional changes over long periods of time—have
been the subject of intensive study and debate in evolutionary science. Large-scale patterns in the history of life have also
been of considerable interest to nonspecialists, although misinterpretations and misunderstandings of this important issue
are common and can have significant implications for an overall understanding of evolution. This paper provides an overview
of how trends are identified, categorized, and explained in evolutionary biology. Rather than reviewing any particular trend
in detail, the intent is to provide a framework for understanding large-scale evolutionary patterns in general and to highlight
the fact that both the patterns and their underlying causes are usually quite complex.
相似文献
T. Ryan GregoryEmail: |
11.
Elizabeth S. Allman James H. Degnan John A. Rhodes 《Journal of mathematical biology》2011,62(6):833-862
Gene trees are evolutionary trees representing the ancestry of genes sampled from multiple populations. Species trees represent
populations of individuals—each with many genes—splitting into new populations or species. The coalescent process, which models
ancestry of gene copies within populations, is often used to model the probability distribution of gene trees given a fixed
species tree. This multispecies coalescent model provides a framework for phylogeneticists to infer species trees from gene
trees using maximum likelihood or Bayesian approaches. Because the coalescent models a branching process over time, all trees
are typically assumed to be rooted in this setting. Often, however, gene trees inferred by traditional phylogenetic methods
are unrooted. We investigate probabilities of unrooted gene trees under the multispecies coalescent model. We show that when
there are four species with one gene sampled per species, the distribution of unrooted gene tree topologies identifies the
unrooted species tree topology and some, but not all, information in the species tree edges (branch lengths). The location
of the root on the species tree is not identifiable in this situation. However, for 5 or more species with one gene sampled
per species, we show that the distribution of unrooted gene tree topologies identifies the rooted species tree topology and
all its internal branch lengths. The length of any pendant branch leading to a leaf of the species tree is also identifiable
for any species from which more than one gene is sampled. 相似文献
12.
Evolutionary trees are key tools for modern biology and are commonly portrayed in textbooks to promote learning about biological evolution. However, many people have difficulty in understanding what evolutionary trees are meant to portray. In fact, some ideas that current professional biologists depict with evolutionary trees are neither clearly defined nor conveyed to students. To help biology teachers and students learn how to more deeply interpret, understand and gain knowledge from diagrams that represent ancestor–descendant relationships and evolutionary lineages, we describe the different rooted and unrooted evolutionary tree visualisations and explain how they are best read. Examples from a study of tree-shaped diagrams in the journal Science are used to illustrate how to distinguish evolutionary trees from other tree-shaped representations that are easily misunderstood as visualising evolutionary relationships. We end by making recommendations for how our findings may be implemented in teaching practice in this important area of biology education. 相似文献
13.
Given the importance of phylogenetic trees to understanding common ancestry and evolution, they are a necessary part of the undergraduate biology curriculum. However, a number of common misconceptions, such as reading across branch tips and understanding homoplasy, can pose difficulties in student understanding. Students also may take phylogenetic trees to be fact, instead of hypotheses. Below we outline a case study that we have used in upper-level undergraduate evolution and ichthyology courses that utilizes shark teeth (representing fossils), body characters, and mitochondrial genes. Students construct their own trees using freely available software, and are prompted to compare their trees with a series of questions. Finally, students explore homoplasy, polytomies, and trees as hypotheses during a class discussion period. This case study gives students practice with tree-thinking, as well as demonstrating that tree topology is reliant on which characters and tree-building algorithms are used. 相似文献
14.
Louise S. Mead 《Evolution》2009,2(2):310-314
A common misconception of evolutionary biology is that it involves a search for “missing links” in the history of life. Relying
on this misconception, antievolutionists present the supposed absence of transitional forms from the fossil record as evidence
against evolution. Students of biology need to understand that evolution is a branching process, paleontologists do not expect
to find “missing links,” and evolutionary research uses independent lines of evidence to test hypotheses and make conclusions
about the history of life. Teachers can facilitate such learning by incorporating cladistics and tree-thinking into the curriculum
and using evograms to focus on important evolutionary transitions. 相似文献
15.
William E. H. Harcourt-Smith 《Evolution》2012,5(1):4-8
The American Museum of Natural History in New York has a rich history of explaining evolution through its displays and educational
programs. For much of this history, there has been a permanent hall dedicated to human evolution and its related disciplines.
Different versions of these halls have informed tens of millions of visitors, and today’s offering is one of the world’s newest,
opened in 2007 and named the Anne and Bernard Spitzer Hall of Human Origins. The hall’s design is radical in that it starts
by giving molecular genetics and the fossil record equal billing and thus provides the visitor with two independent but highly
complementary lines of evidence for our own evolution. Other parts of the hall are innovative in that they stress taxonomic
diversity in the fossil record as much as the more traditional chronological “story” of human evolution that is usually found
in museum exhibits. The hall is also unique in that it incorporates a fully operational teaching laboratory within its architectural
footprint, which provides educators with the chance to seamlessly integrate hands-on lab sessions and the surrounding exhibits
as teaching aids. 相似文献
16.
Meisel RP 《Evolution》2010,3(4):621-628
Evolution is the unifying principle of all biology, and understanding how evolutionary relationships are represented is critical
for a complete understanding of evolution. Phylogenetic trees are the most conventional tool for displaying evolutionary relationships,
and “tree-thinking” has been coined as a term to describe the ability to conceptualize evolutionary relationships. Students
often lack tree-thinking skills, and developing those skills should be a priority of biology curricula. Many common student
misconceptions have been described, and a successful instructor needs a suite of tools for correcting those misconceptions.
I review the literature on teaching tree-thinking to undergraduate students and suggest how this material can be presented
within an inquiry-based framework. 相似文献
17.
The universal ancestor at the root of the species tree of life depicts a population of organisms with a surprising degree of complexity, posessing genomes and translation systems much like that of microbial life today. As the first life forms were most likely to have been simple replicators, considerable evolutionary change must have taken place prior to the last universal common ancestor. It is often assumed that the lack of earlier branches on the tree of life is due to a prevalence of random horizontal gene transfer that obscured the delineations between lineages and hindered their divergence. Therefore, principles of microbial evolution and ecology may give us some insight into these early stages in the history of life. Here, we synthesize the current understanding of organismal and genome evolution from the perspective of microbial ecology and apply these evolutionary principles to the earliest stages of life on Earth. We focus especially on broad evolutionary modes pertaining to horizontal gene transfer, pangenome structure, and microbial mat communities. 相似文献
18.
Evolutionary biology owes much to Charles Darwin, whose discussions of common descent and natural selection provide the foundations
of the discipline. But evolutionary biology has expanded well beyond its foundations to encompass many theories and concepts
unknown in the 19th century. The term “Darwinism” is, therefore, ambiguous and misleading. Compounding the problem of “Darwinism”
is the hijacking of the term by creationists to portray evolution as a dangerous ideology—an “ism”—that has no place in the
science classroom. When scientists and teachers use “Darwinism” as synonymous with evolutionary biology, it reinforces such
a misleading portrayal and hinders efforts to present the scientific standing of evolution accurately. Accordingly, the term
“Darwinism” should be abandoned as a synonym for evolutionary biology. 相似文献
19.
Tal Dagan William Martin 《Philosophical transactions of the Royal Society of London. Series B, Biological sciences》2009,364(1527):2187-2196
Most current thinking about evolution is couched in the concept of trees. The notion of a tree with recursively bifurcating branches representing recurrent divergence events is a plausible metaphor to describe the evolution of multicellular organisms like vertebrates or land plants. But if we try to force the tree metaphor onto the whole of the evolutionary process, things go badly awry, because the more closely we inspect microbial genomes through the looking glass of gene and genome sequence comparisons, the smaller the amount of the data that fits the concept of a bifurcating tree becomes. That is mainly because among microbes, endosymbiosis and lateral gene transfer are important, two mechanisms of natural variation that differ from the kind of natural variation that Darwin had in mind. For such reasons, when it comes to discussing the relationships among all living things, that is, including the microbes and all of their genes rather than just one or a select few, many biologists are now beginning to talk about networks rather than trees in the context of evolutionary relationships among microbial chromosomes. But talk is not enough. If we were to actually construct networks instead of trees to describe the evolutionary process, what would they look like? Here we consider endosymbiosis and an example of a network of genomes involving 181 sequenced prokaryotes and how that squares off with some ideas about early cell evolution. 相似文献
20.
David R. Lindberg 《Evolution》2009,2(2):191-203
The story of the discovery and study of the Monoplacophora (or Tryblidia) and how they have contributed to our understanding
of the evolution of the Mollusca highlights the importance of integrating data from the fossil record with the study of living
forms. Monoplacophora were common in the early Paleozoic and were thought to have become extinct during the Devonian Period,
approximately 375 Mya. In the mid 1950s, they were recovered from abyssal depths off of Costa Rica and were immediately heralded
as a “living fossil.” The living specimens confirmed that some of the organs (kidneys, heart, and gills) were repeated serially,
just like the shell muscles that had been observed in fossil specimens. This supported the hypothesis that they were closely
related to other segmented organisms such as annelids and arthropods. Today, there are 29 described living species and a growing
body of work examining their anatomy, phylogeny, and ecology. Additional fossil specimens have also been discovered, and what
was once thought to be a possible missing link between annelid worms and mollusks now appears to be a highly specialized branch
of the molluscan tree that tells us little about the ancestral mollusk condition. However, some assumptions and generalizations
from those early days still remain—such as the abyssal nature of the living species. A large part of the evolutionary history
of the lineage remains to be discovered and will likely prove more complicated and interesting than afforded by the living
fossil designation. 相似文献