Why Trees Are Important

Abstract

The Tree of Life is the result of the interplay of changes in information and speciation. Almost 100 years after publication of Darwin's Origin, the inception of Phylogenetic Systematics has resulted in a revolution in data inference. I briefly trace the development of this revolution and show examples of how data are interpreted relative to phylogenetic trees. I then provide brief discussions of how to read tree diagrams and the need to access the quality of phylogenetic inference. Keywords Phylogenetic systematics . Phylogenetic trees . CladisticsAs a first principle, we adopt the Darwinian idea that all life is related. Life is diverse, being composed of many species, not one. So while there may have been only one line of descent initially, there are now many lines of descent, many "families" reproducing through time. This means that evolution is not simply "change through time," although it certainly is that; it means, minimally, that speciation is also occurring such that lines of descent are divided by various processes into two or more lines of descent which can then follow their own, independent, evolutionary pathways. I say minimally because speciation mechanisms are diverse, sometimes two lineages found a third through other mechanisms, or one lineage spins off a new lineage through other processes. So we can conceive of the Tree of Life in nature as a diverging hierarchy of lineages composed of one or more populations with a few too many individual organisms, with most of the divergence being caused by the establishment of new lineages through speciation. Thus there are two general processes at work in evolutionary descent. One is change in information; ultimately change in the genetic code and how genes interact during development. When played out over time, this general process is termed "anagenesis" and the mechanisms include natural selection, sexual selection, and genetic drift operating on single evolving lineages. The other general process is speciation, the origin of new species. Although speciation can take many forms (various modes of speciation), these forms involve the establishment of two or more lineages where only a single lineage existed before: an ancestral species gives rise to daughter species through lineage splitting. This lineage splitting has been called "cladogenesis" and this is the origin of the term "cladist."Over the past 40 or so years, a revolution has occurred in the way that many biologists look at data. The revolution is fairly simple but profound. Data are interpreted relative to trees of descent which are the inferred genealogical relationships of entities linked by history. From this perspective, the data are dynamic; information changes through time, and these changes can be studied by following lines of genealogical descent. Trees can depict our hypotheses of the histories of individual organisms, populations, genes, proteins, morphological characters, developmental patterns, species, groups of species, and even areas of the Earth. In short, trees can con...

Evolutionary Trees from the Tabloids and Beyond

“…But there are many more examples of practical and scientific applications of phylogenetics-for example, in classification (as discussed in Mclennan 2010a;Wiley 2010;and Thanukos 2009) and in testing hypotheses about evolution (e.g., see Mclennan 2010b for examples of testing hypotheses about human behavior). Incorporating examples such as these into instruction on evolution can help students view phylogenetics as more than a complicated method of analysis practiced by biologists.…”

“…As summarized by Wiley (2010), in 1995, Schmidt (a medical doctor) was accused of injecting his former mistress (Janet Allen, a nurse) with HIV-positive blood from one of his patients. Allen and Schmidt had been romantically involved for a decade, and Schmidt had been giving her regular vitamin injections.…”

“…Here, we will focus on practical applications of phylogenetics, expanding on one example referenced in another article in this issue (Wiley 2010) and introducing selected additional examples ripe for deployment in classrooms. So what exactly can you do with a phylogeny?…”

Accepting, understanding, teaching, and learning (human) evolution: Obstacles and opportunities

“…Incorporating compelling examples of personal and practical applications of evolution that are relevant to students’ lives and basic social issues may increase their motivation to learn and retain evolutionary concepts (Scharmann, ; Hillis, ; Thanukos, 2010a; Nelson, ; Pobiner, ; Heady and Sinatra, ; Infanti and Wiles, ; Borgerding et al, ; Pobiner et al, ). Examples of evolution related to humans that focus on current topics and everyday experience, such as public and personal health and medicine (the origins of disease and genetic conditions, such as the common cold, sickle cell anemia, malaria, cancer, Huntington's chorea, and human immunodeficiency virus, disease transfer between species such as avian and swine flu, testing pharmaceuticals and skin care products on animals, vaccine development, antibiotic resistance, and the function and prevention of spread of viruses and pathogens); the evolution of high altitude adaptation and lactose tolerance; the evolution of human skin color; the evolution of running; the role of genes in human behavior; genetic engineering; agricultural practices, including the potentially catastrophic impact of a disease on strains of plants and animals that lack diversity, such as the potato famine; how animal hormones can influence biological systems and mechanisms in humans; global climate change, conservation, and species’ vulnerability to extinction; and using evolutionary analyses such as DNA fingerprinting in forensic science to detect crimes or catch criminals can highlight the relevance and applicability of evolutionary theory (McKeachie et al, ; Chuang, ; Scharmann, ; Evans, ; Sinatra et al, ; Varlese, 2008; Werth, ; Pugh et al, ; Thanukos, ; Wiley, ; Andrews et al, 2011; Miekle and Scott, ; Nelson, ; Pobiner, ; Southerland and Nadelson, ; Infanti and Wiles, ; Nadelson and Hardy, ; Pobiner et al, ; Rice et al, ) and the idea that humans are still evolving (Shields, ; Balter, ; Pritchard, ; Andrews et al, ; Pobiner et al, ). Examples that are relevant to students’ lives have been documented to increase students’ attitudes toward evolution, particularly with regard to their perceptions of its relevance (Infanti and Wiles, ; Pobiner et al, ).…”

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“…P hylogenetic trees have a long history of representing evolutionary hypotheses in the printed volume (Figures 1-3). Because they serve as a summary diagram for the tempo and mode of evolution, trees are included in nearly every biology textbook and they are significant tools for teaching hypothesis formation and testing (Wiley 2010).…”