Why do phylogenies always put species as terminal nodes? Is the fossil record too sparse to find/identify common ancestors or is it that we just can’t tell for sure from fossils if the organism was ancestral to another species? Is DNA the only way to have a high level of certainty that something is ancestral as opposed to just related?
(I’m prepping to teach my middle schooler, so the issue may also be that the diagrams I’m seeing are gross simplifications)
Looking forward to the experts answers, but generally, fossils rarely are the actual ancestors, but are more likely related species to the actual ancestor. The reason is that fossilization is pretty rare, and it is more likely you get a cousin than the actual ancestor since their are a lot more cousins. The example given somewhere (wish I could remember where I read it, maybe Adam and the Genome) is that if you went to your ancestoral town ( mine might be on the Isle of Bute, Scotland) and dug up a grave, it would be unlikely to be one of your genetic ancestors, but more likely to be someone who lived at the same time.
And due to divergent and convergent evolution, it is tough to say who is ancestoral to what, but DNA makes it a relative slam dunk, having just watched the NBA finals game. Durant was awesome.
To be expected is that the most abundant part of all phylogenies are the terminal nodes as we have the greatest amount of data on species that currently exist (i.e. are much more easily observable). However, if we were to go backwards in time say 50 million years, the modern/current species would be listed as terminal nodes. But if we were going to overlay the terminal nodes of 50 million years ago, they would be serving as branches in our current diagram. However, as already mentioned, the main way to fill in the tree is through the fossil record (i.e. mostly through the infamous transition fossils). Here is a fun short video on all of those ‘gaps’ that many still contend are missing: Almost Every Single Transitional Fossil Discovered (2017) - YouTube
Genetic evidence is just another impressive growing body of evidence to add to the story of support for ‘macroevolution.’ (29+ Evidences for Macroevolution: The Scientific Case for Common Descent lists many of them though was last updated in 2012). Dr. Venema does an excellent job illustrating common descent from a genetic perspective in the first three chapters of Adam and the Genome. However, this method would be primarily focused on analyzing species that are currently alive, as despite the bond strength of DNA being much higher than the thermal background, it has a finite halflife of approximately 521 years (DNA has a 521-year half-life | Nature). This means that roughly half of the bonds break every 521 years leaving you with very short fragments and a single base pair (assuming you start with 5 million) after just 11,500 years. The Nature article estimates a little longer halflife under ideal conditions but the point is that genetic evidencs is mainly limited to present species (i.e. the terminal nodes of phylogenies).
Hope this makes sense and is somewhat useful. And go Penguins!
Pretty much. Put it this way: if the fossil is too young for reproduction, it almost certainly is not the actual ancestor of anything. And although we may suspect it looks a lot like a suspected ancestor should, there’s no way to tell for sure if the ancestor was its full sibling or a related subspecies from the next valley over or a whole different genus that just had a pretty similar skeleton.
Often scientists will see traits that definitely don’t match up with the expected ones, and then they can be pretty sure that the fossil is a side branch, unless the traits evolved and then were lost, which could happen (depending on the example) but is a little more improbable.
So even if something was suspected to be a common ancestor (or at least in the species that was ancestral), it would probably still be shown as a terminal node because we don’t really have enough evidence to know definitively?
I read Adam & the Genome and it was excellent, as is all of Dennis’s work. But being a non-scientist I’m still trying to wrap my mind around these concepts 
Yep! I’ve seen a few trees that show fossil organisms actually on branches, but they’re not as common.
Keep in mind too that ‘species’ becomes a pretty guesswork concept itself. We can’t know if one fossil was reproductively compatible with a different fossil, so they get lumped into groups based on how similar they are to each other morphologically, and experts are constantly arguing over where, exactly, the boundaries of those groups should fall.
That’s the nature of phylogenetic trees. Every species gets its own node.
Picture a bacterium. It reproduces by splitting into two bacteria. Plot this process with time on the vertical axis. With a single bacterium you plot a single, straight line until the bacterium splits in two. Draw that event as splitting the original line at time = t. Now, one line presents the ‘original bacterium’ and another represents the ‘daughter’. Time progresses and the lines of the two cells elongate. Subsequent reproduction of the various bacteria in the lineage occurs. That results in more splits and new lines in the plot.
If a bacterium dies, its line stops.
Let’s assume you’re scaling the lengths of the tree’s vertical lines to some metric of similarity or time. Also, assume that one fossilized organism was an actual parent of a new species. In that case, you’d still give the fossilized organism a node (separated horizontally). The vertical line for the ‘daughter’ might be short, but they’d still occupy different nodes.
Or think of it this way: Phylogenetic trees are indications of common ancestry and sometimes the length of the branches represent relative similarity or time. They don’t plot exact ancestors. And it’s true that most of the time, one couldn’t precisely identify the exact population of ancestors even if you happened to have their fossils. Most of the time you can only say that they shared common ancestors.
Following the general arc of this thread, I read somewhere (was it on BioLogos?), the Platypus has numerous misconceptions:
It’s salient non-mammalian oddities include:
[[ Not to even mention the odd mixture of mammalian traits such as a beaver-like tail and otter-like feet!]]
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One last comment from me - because of the various borrowings that look like animal groups in preceding branches of ancestral divergences, people have been quick to assume that the Platypus represents normal mammalian features prior to the emergence of the diverging Marsupial v. Placental lineages.
But in fact, the features of the Platypus are distinctive specializations, rather than what they started with. Though I have to wonder if “egg-laying” isn’t still something that they all had when they first differentiated into the earliest kinds of mammals (neither marsupial nor placental).
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[Quoted Material]
“The platypus and other monotremes were very poorly understood, and some of the 19th century myths that grew up around them—for example, that the monotremes were “inferior” or quasireptilian—still endure. In 1947, William King
Keep in mind too that ‘species’ becomes a pretty guesswork concept itself. We can’t know if one fossil was reproductively Gregory theorised that placental mammals and marsupials may have diverged earlier, and a subsequent branching divided the monotremes and marsupials, but later research and fossil discoveries have suggested this is incorrect.”
“In fact, modern monotremes are the survivors of an early branching of the mammal tree, and a later branching is thought to have led to the marsupial and placental groups. Molecular clock and fossil dating suggest platypuses split from echidnas around 19–48 million years ago.” [FN**]
Footnote** Phillips MJ; Bennett TH; Lee MS (2009). “Molecules, morphology, and ecology indicate a recent, amphibious ancestry for echidnas”. URL: Molecules, morphology, and ecology indicate a recent, amphibious ancestry for echidnas - PMC
Also: Proc. Natl. Acad. Sci. U.S.A. 106 (40): 17089–94. doi:10.1073/pnas.0904649106. PMC 2761324 Freely accessible. PMID 19805098.
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"A multigene evaluation of the ((echidna [i.e. placental] [vs.] platypus)) divergence using both
“Platypus-like monotremes (Monotrematum) predate this divergence, indicating that echidnas [animals from the weird ant-eater group] had aquatically foraging ancestors that reinvaded [. . . migrating up and out of the water into …] terrestrial ecosystems. This . . . shift and the associated radiation of echidnas [ant-eaters] represent a recent expansion of niche space despite potential competition from marsupials.”
“Monotremes might have survived the invasion of marsupials into Australasia by exploiting ecological niches in which marsupials are restricted by their reproductive mode.”
[i.e. Baby pouches and swimming in water don’t mix!!.]
“Morphology, ecology, and molecular biology together indicate that Teinolophos and Steropodon are basal monotremes rather than platypus relatives, and that living monotremes are a relatively recent radiation.”
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