The Bush of Life: Cladistics for the Layperson

Have you heard the news?  Birds are reptiles.  Insects are probably crustaceans.  Those hydrothermal vent worms are annelids.  Water lilies are more special than we ever realized.
All of these improved understandings of where various organisms come from a key innovation in how biologists approach and think about evolutionary relationships.  That innovation is called cladistics, and it remains far, far more poorly understood than the hierarchical system it replaced in the 1990s.  Many have tried to fix that, including the inestimable Dr. Thomas R. Holtz, Jr.  This is my grain in that silo.

Daft King Philip Came Over For Good Sex, Seriously

I picked up this mnemonic at the University of Miami, after cycling through a few shorter and less cheeky versions.  It’s a classic that has followed biology students since the 1950s, if not longer, helping us memorize the Linnaean classification hierarchy: domain, kingdom, phylum (division for botanists), class, order, family, genus, species, subspecies.
Here’s what it looked like for one of my favorite animals, the peacock mantis shrimp, and one of Ania’s favorite animals, New Zealand’s carnivorous parrot.
Peacock Mantis Shrimp
Organisms with nucleated cells
Jointed-limbed animals
Animals with notochords
Mantis shrimp
New Zealand parrots
Peacock mantis shrimp



This system has dominated biology textbooks for decades, and its inventor, Carl Linnaeus, is among the national heroes of Sweden.  His most famous work, Systema Naturae, popularized the idea of “binomial nomenclature,” wherein the genus and species ranks above can serve together as an unambiguous identifier for a species, so his honor is well deserved.  Based on a rigorous analysis of morphology, reproductive behavior, and other attributes, the Linnaean categories have, by and large, withstood a great deal of scrutiny.  Even after much more detailed examination using modern genetic techniques and incorporating organisms unknown in Linnaeus’s time, many of the more obvious groups persist.
The overall scheme, however, has proven very problematic.  The Linnaean scheme is based on overall similarity, a difficult-to-quantify metric that often fails to reflect evolutionary history.  A common failing is that highly specialized organisms will be grouped separately in a way that obscures their actual relationships with other groups.  Because evolutionary relationships have predictive power, this means the Linnaean system hides from laypeople and scientists alike ways in which seemingly disparate organisms are actually similar to one another, ways that have turned out to have medical and ecological relevance for humans.  It also hides a subtler distinction, to be explored later.
Another problem is that the Linnaean system has specific, named ranks.  Animals are a Kingdom, equal in prominence to the other Kingdoms; insects are a Class, at the same level as the other arthropod classes like Arachnida.  Different ranks often have different associated suffixes: animal orders often end in –iformes, families end in –idae for animals and –aceae for plants, superfamilies are usually –oidea, and so on.  These conventions can simplify conversations about various groups, since the level of organization is already given by the ending of its name.  However, this means that, if a group’s rank changes, its name and the names of all of the groups within it can also change.  Previous such changes have massively complicated the process of following the scientific literature on revised groups, to say nothing of books written for lay audiences.
Birds provide an emblematic example of both of these problems.  In the Linnaean system, birds are a class unto themselves, Aves, because of the numerous anatomical and behavioral traits they share with each other but not with other living vertebrates.  However, the evolutionary history of birds traces down a line of progressively more “reptile-like” feathered animals until it blends seamlessly into a famous lineage of carnivorous dinosaurs, and from there into creatures well-established as “reptiles.”  Along the way, may of birds’ famous skeletal peculiarities emerge progressively, rather than all at once.  Early bird ancestors have feathers and but otherwise resemble non-feathered dinosaurs.  Later on, fossils appear that have the birds’ characteristic fused tail vertebrae but still have claws and teeth.  The fossil record shows that, while modern birds are highly dissimilar from other vertebrates, their ancestors were much less divergent, and obviously reptilian.
A Linnaean answer might be to preserve birds as a separate group, because of their modern weirdness, and effectively ignore the fossil record’s suggestion that early birds were not quite so unique.  This approach hides the evidence of relatedness between birds and modern and fossil reptiles, evidence that helps explain a number of avian quirks, such as birds’ scaly, four-toed feet and markedly different lung physiology from mammals.  Another Linnaean approach might instead take this relatedness into account and incorporate Aves as a subclass or order within Reptilia, demoting Aves’s constituent groups accordingly.  Since Aves contains over 10,000 species and was previously divided into 23-30 orders and over 40 families, this would massively alter the vertebrate classification scheme as it is commonly understood.  Depending on how it was done, might also require changing dozens of suffixes, in particular the –iformes endings of avian orders.  Such a system would reflect evolutionary relationships a little more accurately, but would render the revised system opaque to people who relied the old one.
Such revisions were once common.  The Linnaean tiers students memorize with catchy mnemonics have been supplemented with a dense tangle of subsidiary categories: subphyla, superorders, infraclasses, subgenera, and tribes (between family and genus), each with characteristic suffixes, now fill the gaps between the larger divisions, enabling taxonomists to recognize that vertebrates share a kinship with salps and lancelets without demoting vertebrates to a class, reptiles to an order, and so on.  Instead, vertebrates became a subphylum of Chordata, and the vertebrate classes and orders were unmoved.  This is particularly important when lower levels are revised, since the “species” level has ecological significance separate from its role in the tiered Linnaean classification scheme.
As knowledge of evolutionary relationships and the similarities that they reveal has increased, these extra tiers have become similar to the epicycles that once patched the holes in geocentrism, layers upon layers of additional complexity required to make an ultimately untenable model hold together.  In order to make good on Charles Darwin’s prescient suggestion that “our classifications will come to be, as far as they can be so made, genealogies; and will then truly give what may be called the plan of creation,” a new practice would be needed.

Grades and Clades

The modern system of classification has two important differences from the older system that most of us encountered in grade school:
·         Common descent, not similarity, is the criterion for valid groups.
·         Groups are no longer assigned ranks.
Common descent, in the cladistic model, has a very specific definition.  A cladistically valid group is defined as a specific common ancestor and all of its descendants, and is identified based on sharing with those descendants one or more specific traits that they do not share with other putative relatives of theirs. This trait(s) is the difference that enabled this ancestor to distinguish itself from its own relatives and to radiate into those descendants in the fullness of geologic time.  The ancestor’s other traits, those it shares with its own ancestors, are known as shared primitive traits.  This distinction forms the core of the difference between the older classification scheme that still populates elementary-level textbooks and the new one.  In cladistics, primitive characters are recognized as not useful for resolving the relationships between the organisms that have them.
To put it another way:
Suppose one of your distant ancestors acquired an enormous sum of money, which your family has kept in well-conceived investments (so that, for illustrative purposes, it never runs out).  All of that ancestor’s descendants have the same level of access to this pile of money, including you.  One side effect of this scenario, aside from your being able to use Rolls Royce-mounted belt-fed Gatling guns with depleted uranium slugs to hunt the genetically engineered dodoraptors on your private island in space, is that, when you tell someone you’re from the Cashington family, that doesn’t actually tell them a whole lot about your ancestors.  That doesn’t tell them whether you’re one generation or 30 removed from the Cashington p/matriarch who acquired that initial windfall, and it doesn’t tell them whether your grandparents are of the Bali Cashingtons or the Tierra del Fuego Cashingtons.  More importantly, if you meet another Cashington, knowing that you’re both Cashingtons doesn’t tell you whether your Uncle Yen and Aunt Renminbi Cashington are their cousins or parents or siblings.  Access to the Cashington family fortune is, in this example, a primitive character.  Access to the Cashington fortune defines the Cashingtons as a distinct group, and as a result, it does not in and of itself illuminate the relationships between the Cashingtons.
But suppose that your great-great-grandparents, in addition to having the usual Cashington bank pass, started tattooing themselves with a unique symbol—say, a budgerigar holding an axe, in the style of the Kenyan Coat of Arms.  They insist on their offspring getting this tattoo, and it becomes a family tradition, unfailingly passed on through the generations of their descendants.  Now, when you meet another Cashington, you can find out how close you are to them by checking whether they have the Parakeet Viking Rampant on their left shoulder.  If you meet another person, you can find out whether they’re a Cashington via their access to the Cashington fortune, and you can find out whether they’re a Parakeet Viking Rampant Cashington by checking for the tattoo.  The people of the Parakeet Viking Rampant are an identifiable subgroup of the Cashingtons, and knowing that someone bears the PVR tattoo reveals information about their place in the overall Cashington family tree.  Possession of the Parakeet Viking Rampant is a shared derived character, in cladistic parlance.
Let’s take that thinking to the vertebrate family tree, in particular the same avian example we have already considered.
As noted earlier, Linnaean diagrams of the vertebrates usually designate mammals, birds, and reptiles as the three major classes of land vertebrates.  Reptiles, as a group, are generally united by their shared possession of keratinous scales, a physiology dependent on external heat sources, and leathery eggs.  However, consulting with the fossil record and taking other traits (such as bone structure) into account reveals that these traits are all primitive.  All of them are the original, ancestral state for land vertebrates, including the lineage that gave rise to mammals.  This suite of characters therefore is not helpful in defining mammals, turtles, birds, or any other sub-group of land vertebrates as distinct from the others, any more than access to the Cashington fortune reveals anything about where in the Cashington family tree a particular Cashington sits.  Indeed, all signs point to the last common ancestor of all creatures colloquially known as reptiles also counting, among its descendants, all mammals and birds.  If reptiles are to be a valid group by modern standards, they must include mammals and birds, and “reptile” must become synonymous with “land vertebrate” or (more precisely) “amniote.”
In order to resolve the relationships between the amniotes, additional traits must be sought and taken into account, vertebrate answers to the Parakeet Viking Rampant.  These skeletal, genetic, and anatomical innovations have replaced the idea of “reptiles” with a series of more precise identifiers.  Now, we have:
·         Amniotes: Animals with a certain set of membranes supporting their embryos, including modern mammals, turtles, lizards, snakes, tuataras, crocodilians, and birds and their extinct relatives.
o   Diapsids: Animals with amniotic eggs and two sets of temporal fenestrae, holes in the skull through which the jaw muscles attach, including modern lizards, snakes, tuataras, crocodilians, and birds and their extinct relatives.  Mammals and their ancestors have the synapsid condition, with one set of temporal fenestrae.  Turtles have no temporal fenestrae, but genetic tests sometimes associate them with the diapsids.
§  Archosaurs: Animals with amniotic eggs, two sets of temporal fenestrae (often lost or fused), and teeth set in sockets rather than on the surface of the jawbone, including modern crocodilians and birds and their extinct relatives.  Lizards, snakes, tuataras, and extinct groups like plesiosaurs form other diapsid lineages, such as the Lepidosauria.  Birds, among their numerous other specializations, do not grow teeth as adults, but still have the genetic information for odontogenesis.  Archosaur tooth sockets are not the same as the similar sockets found in modern mammals.
·         Coelurosaur dinosaurs: Animals with amniotic eggs, two sets of temporal fenestrae (sometimes fused), teeth set in sockets (lost in modern forms), and feathers.  Modern birds are a subset of this group.
Two caveats should be emphasized: 1) This outline-form cladogram is incomplete, and leaves out some branches and categories for space and clarity; and 2) the traits given here as defining the major branches are not a comprehensive list, and modern groups have an abundance of traits, especially genetic markers, bolstering their case.
Now, the entire system is designed to generate trees that can serve as testable hypotheses about the evolutionary history of life on Earth.  The task of the taxonomist has moved past merely cataloguing the world’s diversity, and into the far more rewarding task of making predictions about it.  Cladistics has revealed strange new facts about the skin of arthropods that may lead to new kinds of pesticides; led to insights into how respiratory and circulatory systems work; and made excruciatingly clear just how deeply into the mammalian family tree the human race truly sits, as only the narrowest categories keep humans apart from our fellow apes.  Applying the same methods to linguistics and archaeology has granted improved understanding of human migrations and reminded us that we are all kin in other ways.
Evolutionary biology underpins such a staggering fraction of humanity’s accomplishments that its impact as an idea and as a phenomenon cannot be overstated.  The cladistic method has been part of that impact, a piece of humanity’s scientific heritage whose importance is only now being realized, and whose reverberations will continue to revise our understanding of the relationships between organisms for centuries to come.
And since trying to explain that to the first-year students I teach every year is an exercise in confusion and terror, I wrote this.  May the Cashingtons and their Parakeet Viking Rampant forever undergird their understanding.
The Bush of Life: Cladistics for the Layperson

Shifty Lines: South Asia

This installment of Shifty Lines takes us to another region of Asia.  After looking at ethnolinguistic divides in north Asia, the Persosphere, and the Caucasus, we move now to the region known variously as the Indian subcontinent, “India,” and (most correctly) South Asia.

A Succession of Empires

South Asia has been the seat of empires throughout its history, starting from before the Indo-Aryan invasion with the Indus Valley Civilization.  Almost universally based in the north, these empires differed in how far into the subcontinent they conquered.  The early Mahajanapadas only edged into southern India, while the Maurya and Gupta Empires controlled virtually all of South Asia, including the Maldive Islands.  The rest of the time, southern, Dravidian India was independent under the Chola, Chera, and Pandya dynasties, with the Cholas managing to conquer much of India and parts of Indonesia and Southeast Asia in the 10th century CE as well.  Sri Lanka was part of some of these South Indian empires, establishing a Dravidian minority alongside its Indo-Aryan majority.  During these periods of empire, the characteristic native religions of South Asia, Hinduism and Buddhism, became established, with Buddhism spreading into East and Southeast Asia as well.
Empires based in South Asia rarely crossed the Himalaya and Arakan mountains that separate modern India from Burma and China, while their borders with the Persian Empire were much more fluid.  The Himalayan regions of Nepal and Bhutan likewise retained their independence throughout most or perhaps even all of these imperial periods.  Thus, while the empires of India were the equals of any of their better-known neighbors and trading partners, they did not succeed in conquering a region vastly outside the currently recognized boundaries of South Asia.  These geographical limitations set up the next phase of India’s history: the Muslim conquests.
Between the 7th and the 15thcenturies CE, South Asia faced repeated invasions from Muslim powers, including the Umayyad Caliphate that conquered Spain.  The combination of invading armies from Persia and Central Asia and Arab mariners establishing trading posts along India’s western coast introduced Islam to India, which would eventually become home to one of the world’s largest concentrations of Muslims.  Numerous kingdoms became sultanates ruled by Persian and Central Asian conquerors, most notably in Delhi, while the south responded by uniting into the Hindu Vijayanagara Empire to repel further attackers. 
Muslim dominion in South Asia culminated with the Mughal Empire, during which Central Asian conquerors gained control over almost all of South Asia extending into Afghanistan and even further northwest, while never penetrating the southern tip of the Deccan.  Like many ancient empires, the Mughals exerted their power through vassals and tributary states, rather than having direct control over their vast holdings.  This decentralization, combined with Mughal appreciation for South Asian culture, led to the development of numerous syncretic and idiosyncratic forms of Islam in South Asia, many of which persist as the majority religions of various South Asian groups to this day.  Still, Islam was still widely viewed as a foreign intruder in Hindu-majority India, especially when subsequent Mughal rulers began rigidly enforcing Islamic norms and legally penalizing non-Muslims.
The Mughal period collapsed into a series of smaller empires much like the ones that had preceded them.  Former vassal states became ascendant, conquering virtually the entire region over the ensuing century.  In particular, the Maratha Empire emerged from central India to usurp Mughal control over most of South Asia, and the Sikh Empire became a formidable military force that conquered Punjab, Kashmir, Himachal, and nearby regions.  The Marathas were the last Hindu empire to rule in India, and their navy kept Arab, Portuguese, and other invaders at bay until the British conquest.
{Warning: This is a LONG one.}

Continue reading “Shifty Lines: South Asia”

Shifty Lines: South Asia

No Cure For TMD

Start with “prone to sudden fits of neon pink geometric-shape hallucinationsthat cause pain when you look directly at them and grow in size when they’re ignored.” Then add “your jaw tightens until you wonder if rigor mortis is setting in early” and “you want to throw up but actually throwing up makes it feel worse instead of better if it changes anything” and “light and sound make all of the above worse somehow.”
The frequency of the above is based on posture and whether you’ve stretched your rhomboids in exactly the right schedule in the past two weeks so that they take some of the tension out of your neck. If you stretch too often, they get sore and you can’t use that to help prevent the next attack. Too little, and you will hasten the next attack.
Having some kind of stress-relieving fun can help too, which means that these events are often conveniently timed for whatever is most important that you get done or least like doing or are most terrified of screwing up or some other stress-related marker. So you’re as close to peachy as you ever are when it’s time for fun and games, and lots of people think you’re making it up to get out of unpleasant tasks. Which is pretty easy, since “painful hallucinations” don’t exactly make a person leak fluid or emit word salad. They just make it so that eventually you can’t see because your entire visual field is replaced with a pulsating neon pink dimension of pain and nausea and it gets worse every time someone says something within a mile of you. So you sometimes feel a need to exaggerate symptoms like nausea that more people understand even if you could otherwise keep them under control, so they believe you’re sick at all and don’t make an issue of you taking that soul-saving nap.And in every single waking second that that’s not happening and also the ones where it is, your jaw joints and the muscles immediately above them that move your jaws are sore like you spent the past 10 hours chewing a piece of latex that is made of hand grenades, and the question is not “will it hurt today” but “will it hurt enough to be distracting today?” So you spend a lot of time seeing how many fingers wide you can stretch your mouth, to reset some of those muscle fibers and earn two or three seconds of your jaw not being on fire. And also you keep your hands cold to use as impromptu cold-packs. And sometimes you think about shaving the sides of your head so that your hand-packs work better.
And if you sleep in a weird position, you can guarantee one of those “distracting” days will start within about 60 minutes of waking up, even if you went to bed to get rid of the hallucinations. And even if it doesn’t, the disruption to your sleep cycle will make you miserable and lethargic anyway.
And the only painkillers that work are large doses of NSAIDs that make sure that every particularly bad attack is followed by a brutal stomachache. Or you could nap, which is still kind of weird to do on university lounge furniture and takes a fair bit longer.
And you know—KNOW—that you brought almost all of that on yourself by clenching your teeth a lot when you were a kid, since most of those symptoms are based on a repetitive stress injury to the jaw joint and the rest are genetic.
That’s my life with chronic pain.
No Cure For TMD