This post covers chapters 16 & 17 from Futuyma & Kirkpatrick’s book on Evolution (2018). The author of this post is Sam Shry.

Phylogeny: how we are all connected

We know that we look different from a crocodile (well, most of us), but how did we diverge from our common ancestors millions of years ago? Can we trace back our common ancestry and how we are related to every other organism on this planet via our genetic relationship and morphological characteristics? That’s what phylogeny tries to understand and with the help of modern genetic analysis, this process has opened our eyes to understanding the phylogenies of every species.

By backtracking each species’ ancestry, we can understand how they are all related and can determine when species split based on morphology, derived features, and genetic architecture. Understanding the exact order of evolution among species can be tricky, as mutations can occur repeatedly, creating sometimes the same evolved characteristics multiple times in multiple phylogenies (homoplasy). One example is the evolution of winged insects. It is a convoluted mess of where and when each species developed or lost wings, making the phylogenetic tree hard to disentangle when basing the entire analysis only on the presence or absence of wings. To avoid these issues, it is important to analyze more than one characteristic when determining relationships and by combining different tools for analysis (morphological differences, genetic differences, etc.). It also depends on the temporal scale; recent evolutionary differences need to be analyzed using faster-evolving parts of the genome, whereas longer time scales require slower-evolving genome sections. What is also important to remember is phylogeny and genealogy of species may not match up completely as groups of genes can be copied and inherited even with speciation, called incomplete lineage sorting. There can also be problems like introgression, where regions of one genome are taken from another species via hybridization, horizontal gene transfer, etc., which can give a misleading picture of the species’ genome. The best way to avoid these problems with differentiating species is to analyze larger regions of the genome to detect more variability between species.

DNA sequencing is done in multiple ways, but one of the most common ways is parsimony, examining how different species are related to one another based on their genetic base changes, simply put, the phylogenetic tree requiring the fewest evolutionary changes. It can, however, do a bad job of parsing the exact phylogeny of where and when individuals split into new species. More robust, statistical methods such as likelihood estimations and Bayesian inference do a better job of differentiating species exactly where and when points of speciation occur. Though, DNA sequencing is difficult when DNA is hard to come by, as with extinct species. This is when old-school methods are still used to construct phylogenies from morphological data instead. In both methods, we are trying to pinpoint the exact time in history when evolutionary changes occurred, so understanding the “when” is an important aspect. We can do this by analyzing the molecular clock within DNA sequences as we have learned about previously, giving us a rate of sequence evolution, which can be used to estimate the time of divergence. Understanding when and where evolutionary changes occurred gives us a road map to exploring reasons for divergence.                           

We can use phylogenies to answer questions about mutations, adaptations, and genetic variation in general. One example is the three-spined stickleback, which has invaded freshwater systems of almost all reaches of the Northern Pacific and Atlantic oceans. Their variation in armored plates along their back is quite diverse and has been traced back to a single locus, creating this adaptation throughout freshwater populations. Phylogenies can also be used to trace almost any species’ characteristics, such as language, tails, and even virus prevalence. Phylogenies can be compared to one another, especially when investigating adaptions. Investigating the adaptive coupling of characteristics while controlling for phylogenetic relations is a valuable tool for understanding the evolutionary relationship between species’ characteristics.

Figure 1. Three-spined stickleback, Gasterosteus aculeatus. Photo by Jack Wolf

Of course, one of the main purposes of developing phylogenies is to classify species into groups and taxa, as has been done from Aristotle, to Linnaeus to Darwin, to modern phylogenetic classifications. Conveying the relationship between species is an important step to understanding biodiversity and leads to further exploration of genetic architecture passed down within and between species. 

The history of life… really, that’s the title

A bold title and difficult to summarize into two pages, the underlying connection between today and earth hundreds of millions of years ago are the species that have inhabited this planet over time. We can follow a species through time using their fossils as stepping stones in their evolution, while simultaneously trying to understand how the earth’s environment has changed and impacted species’ biodiversity. As the earth has changed, for example via plate tectonics, the layering or strata of sediment holds records of past organisms and gives us the ability to set a time scale to when organisms were found and when they were lost. These fossils are highly valuable, but very difficult to come by, making our fossil record patchy and incomplete. After the “big bang” 14 billion years ago (Gya), biotic “Life” was formed by abiotic chemical reactions (around 3.5 Gya), creating simple organic molecules. The formation of molecules that could replicate independently (most likely RNA) allowed for evolution by natural selection to begin to shape variation. The complexity of life continued to expand and develop over billions of years, from asexual unicellular to sexual unicellular to multicellular organisms. The Precambrian era (Table 1) brought about evolved photosynthesis and oxygen to the atmosphere, as before this period all life (prokaryotes from the groups Archaea and Bacteria) were anaerobic. The emergence of eukaryotes also occurred (1.8 Gya), opening greater possibilities for diversity.

Table 1. Each step in organic life history and a few important evolutionary points from the millions of years in between.

Time periodImportant stuff that happened
Precambrian: 2.5 Gya – 541 Mya-photosynthesis evolved
-oxygen to atmosphere
-emergence of eukaryotes  
Cambrian: 541 Mya – 485 Mya-explosion of diversity
-development of the genetic toolkit for animals
-vertebrates arise
-ended with large extinction event
Paleozoic: 541 Mya – 252 Mya-species diversity
-evidence of modern phyla
-movement to land and terrestrial animals
-plant diversity and terrestrial modifications
-early ancestors of mammals
-ended with mass extinction
Mesozoic: 252 Mya – 66 Mya  -age of reptiles
-break up of Pangea
-slow recovery of diversity
– adaptive radiation
-angiosperms and insect diversity
-End with mass extinction via asteroid impact
Cenozoic: 66 Mya – today-modern time
-closely related ancestors to modern day organisms
-recovery and increased diversity
-forming of modern continental geography and climate
-adaptive radiation of mammals
-human speciation

The Cambrian era of only about 55 Mya, but created large-scale animal diversity by introducing many new species and classes of animals. This explosion of diversity is attributed to new feeding abilities and novel ways of living. Ecological changes, such as increased atmospheric oxygen and a warmer climate could have also helped in the rise of diversity. More diversity during the Paleozoic period meant an increase in aquatic organism diversity, creating larger and more complex invertebrates and vertebrates. Large squids, sea stars, and molluscs were conceived and some of the first reefs were built by two coral groups. The large extinction event during the late Cambrian gave rise to large-scale diversification with new phyla with new ways of life. Boney fish also arose during this time, creating the ancestors of today’s fish species. Aquatic plant diversity also exploded and advanced to form terrestrial plants with roots that form in the newly acquired terrestrial biomass of organic soil. Insects soon followed, as herbivores feeding on terrestrial plants. The transition from fish to tetrapod to terrestrial vertebrates also occurred during this time, moving from fin to limb. At the end of this era however, a mass extinction event occurred as land masses redistributed themselves, creating chaotic and unfavorable living conditions for many species. The Mesozoic era brought about more stable conditions for living and allowed for yet another round of adaptive radiation and diversification with the rise of new reptile species, both marine and terrestrial. Insects and plants diversified, with angiosperms bringing about insect diversity. There was an explosion in terrestrial insect diversity and the sheer size of some is mindboggling, for example, the Arhropleura, a millipede that reached 2.3m long. Birds also came to be with the diversity in reptiles leading to their wing adaptations for flight. The end of the period is marked by another mass extinction due to the impact of an asteroid off the coast of the Yucatan Peninsula, blocking the sun and creating a long-lasting winter. After that, the Cenozoic era begins around 66 Mya and marks the modern time in evolutionary history. The period is marked by the forming of modern-day continents, climate, and species diversity. The re-diversification formed what are today’s species and the radiation of mammals, eventually leading to the speciation of humans. During this period we also see the first indications of human impact on species diversity, with the extinction of what were called megafauna or large-bodied mammals such as mammoths.

As we can tell from this chapter, life has been ever shaped by the climate and environmental changes on Earth, era after era. Extinctions give rise to adaptive radiations with new species adapting to the present environmental conditions and ever-advancing in complexity. Though today, many of the extinctions occurring are due to human impacts. From our microscopic time span of existence, we are causing rapid global change to both environments and biodiversity. We will just have to see how evolution and Earth sort us out over the next million years…