Bi1e Evolution of the Biosphere

Lecture 2: Systematizing life

2.1 Taxonomy
2.2 Homology
2.3 Making trees: cladistics
2.4 Molecular phylogenetics
2.5 The molecular phylogeny revolution

Instructor: Joe Parker, PhD

Beckman Behavioral Biology Room 226
[email protected]
2.1 Taxonomy

Bacteria
Protists Plants
Chromista 435,000
Fungi
Mammals
6,400 spp
Birds Fish Insects
Reptiles
~ 1 million species
Amphibians
8,000 spp
2.1 Taxonomy

Evolutionary Biology
Relationships, species differences,
palaeontology & earth history

Taxonomy:
naming and describing new species, genera or higher
“taxa” (tribes, families, orders, classes, phyla…)

Ecology Organismal biology

Populations, biological Anatomy, embryology,
communities, physiology, neurobiology, behavior
Interactions
2.1 Taxonomy

Describing a new species…

“The name or nomenclatural act must

have been published”

“be accompanied by a description or

definition that states in words
characters that are purported to
differentiate the taxon”
2.1 Taxonomy

Carl Linnaeus, 1758

10,000 species of organisms:

~6,000 plants
~4,000 animals
2.1 Taxonomy

Carl Linnaeus, 1758

Antenna necklace-like

Elytra “halved”

Tail simple

Two oblong cells

2.1 Taxonomy

necklace
Staphylinus

-like
“halved”
simple
Two
oblong
cells
2.1 Taxonomy

Linnaeus’s
microscope
2.1 Taxonomy

Raffray, 1894

143 words
2.1 Taxonomy

Raffray, 1890
2.1 Taxonomy

Jubogaster towai Parker and Maruyama

Jubogaste r gen. nov.
Type species. Juboga ster towai sp. nov. her e designa ted.
Dia gnosis. Eup lectite pselaph ines with the following characters: transverse hea d articulating ventrally und er pro notum when deflexed, typ ical of Trogastrini. Head with vertex excava te, lacking vertexal fovea; ventral hea d with out
the typ ical den se “gen al bea rd” of setae common to most Trogastrini. Eleven-segmented moder ate ly gen icula te antenn ae, received by larg e excava tion s anterio r to eyes. Pro notum jubin e-like: bro ad and obcord ate, constr icted at
basal qua rte r, with weakly-evident medial long itud inal sulcus and distinct anteba sal sulcus. Pro notum afoveate, with margin s smooth, devoid of crenula tion s or small spines found in other Trogastrini. Elytra lacking any ste reotyp ical
fovea. Leg s with contiguous, pro jecting coxae, bro ad femora, basally flatten ed tibia, and three tarsal segments; segment 1 very small, 2 and 3 elon gate and subequ al in leng th. Tarsi with two equ ally-size d claws, unlike other
Trogastrini which have une qually-size d claws. Bifid anterio r pro tar sal claw in the typ e species J. towai.
Ety mology. A combination of Jubus Schaufuss and Trogaster Sha rp, the typ e gen era of Jubini and Trogastrini, respective ly. The name is chosen on account of the membership of the new gen us in Trogastrini, despite app arent
Jubini-like characters such as the shape of the pro notum and the pre sen ce of two equ ally-size d tarsal claws (a character sta te found in Jubini, but not other Eup lectitae). The bifid anterio r pro tar sal claw of the typ e species J. towai
is also shared with Pha misus myrmophilus Silvestr i of Jubini.
Description. Bod y larg e (5.1mm for the typ e species J. towai shown in Figure 1). Bod y shape app roxima tely ovoid and str ongly convex.
Head: App roxima tely triangu lar, str ongly transverse (Fig 4). Ver tex afoveate, concave, with moder ate ly dee p excava tion extending from basal qua rte r to anterio r margin of frons; excava tion nar rowing apically alon g midline as it
passes between raised frontolateral margin s. Frontolateral margin s carinate, extending rou ghly arcuately from posterior of antenn al insertion cavity to clyp eus (Fig 5). Frontolateral face accommo dating larg e circular cavity anterio r
to eyes to receive antenn ae (Fig 5). Eye flanked dire ctly anterio rly by add ition al larg e excava tion for retracted maxillary palp us (Fig 5). Ven tra l surface of hea d bisecte d by long itud inal gula r carina situ ate d with in bro ader gula r
sulcus terminating in gula r fovea. Gu lar sulcus widens basally, spannin g the hea d-neck interface. Maxillary palp i app arently 4-segmented, with segment II long and curved at ape x, III short and triangu lar, wider than II, IV oval,
app roxima tely 2x long er than wide (Fig 5). Antenn ae (Fig 3) with 11 antenn omeres, moder ate ly gen icula te with enla rged segment I. Antenn omeres IX–XI str ongly elon gate (XI long est).
Thorax: Pro notum (Fig 4) obcord ate, 2x wider than hea d, almost as wide as elytra. Afoveate, with smooth margin s. Anterio r margin bro adly arcuate, larg ely obscuring the deflexed hea d when viewed from abo ve, and constr icted
sharply in basal qua rte r, so that pro notum is laterally expand ed into bro ad, blun t spurs with curved edg es. Medial long itud inal sulcus pre sen t on pro notal disc, weakly impressed, thin, terminating at dee per, bow- shaped anteba sal
sulcus that extends between bases of mediola ter al spurs. Pro sternu m afoveate, with lateral long itud inal carinae extending from sides of neck to base. Mesoster num with median mesoster nal foveae (MMSF), lateral mesoster nal
fovea (LMSF) and lateral mesocoxa l fovea (LMCF) pre sen t. Other typ ical pselaph ine mesoster nal fovea liste d in Chandle r (200 1) lacking. Metaster num str ongly convex. Latera l metathoracic foveae (LMTF) pre sen t; median
metathoracic fovea (MMTF) absent.
Abdomen: Abd omen with tergites str ongly convex. Visible segments 1–3 (IV–VI) subequ al in leng th (Fig 1), segment 4 (VII) long est (no t app arent in Fig 1 due to curvature of abd omen). Tergites 1–3 (IV–VI) with pro nounced
par ate rgites, 4 (VII) with small taperin g par ate rgites. Tergite 6 (IX) interna lised. Six ste rnites visib le (Fig 2), ste rnite 7 (IX) interna lised. First visib le ste rnite (III) with median pro cess pro jecting between metacoxa e. Sternites 2 and 3
(IV and V) subequ al in leng th, 4 (VI) slightly shorter (Fig 2).
Elytra: Strong ly convex, slightly bro ader than pro notum (Fig 1), app roxima tely 0.3x total bod y leng th. At their long est, equ al in leng th to visib le abd ominal segments 2+3 (V+VI) combined. Elytral humer i bro adly rou nded to almost
half elytral leng th. Sutura l str ia entire; lacking sutural fovea and other ste reotyp ical anteba sal fovea. Lacking subhumer al fovea and subhumer al str ia. On e weakly defined , somewhat discal dep ression is evident halfway between
suture and humer us; its homolo gy to canonical pselaph ine anteba sal elytral fovea is unclear.
Legs: All coxae contiguous (Fig 2), pro coxae conical, pro jecting ventrally, mesocoxa e glob ose, metacoxa e (Fig 7) transverse-conical, spannin g from ventral midline to metaster nal margin , and pro jecting posteriorly. Femora
somewhat thicken ed, and excava ted apically to receive retracted tibia. Tibia flatten ed basally. Femora and tibia lacking spines or pro cesses. Tarsi elon gate, 3-segmented, first segment extremely short, 0.2x the leng th of segment
2. Seg me nt 2 and 3 subequ al in leng th. All tarsi with 2 well-develop ed, equ ally-size d tarsal claws. Bifid anterio r pro tar sal claw in typ e species J. towai (Fig 8).
Jubogaste r towai sp. nov.
type ma terial. Holotyp e, male, Per u, Satipo, San ta Ana , 25 I 201 2, with Phe idole xanthogaster Wilson. Spe cimen dep osited in Field Museum of Natural History, Chicago, IL, USA, with catalog numbe r: FMNH-INS 000 0 093 389.
Dia gnosis. The sole known species of Juboga ster is high ly distinctive among Trogastrini due to its gre atly enla rged and rob ust bod y covered in thick, blun t gold en setae, the uniq ue concave hea d that lacks vertexal fovea, the
larg e, circular excava tion s on the frons that receive the long , gen icula te antenn ae, the absence of a gen al bea rd, an afoveate pro notum and elytra, the two equ ally-size d tarsal claws, and the bifid anterio r pro tar sal claw.
Ety mology. The new species is named in hon our of Towa Shimad a, son of Taku Shimad a, a remar kab le collecto r of myrmeco philes.
Description. Bod y leng th 5.1mm (Fig 1). Colour dar k red dish bro wn, antenn ae and legs somewhat lighter.
Integument shiny. Most dor sal reg ions covered by conspicuous thick, ere ct, blun t gold en setae, arr anged at reg ularly spaced intervals and orie nta ted posteriorly (de picted most clearly in figures 4–6). These are interspersed with
shorter pub escence of the same colour, also orie nta ted posteriorly. Ven tra l surfaces covered with fine, mostly aciculate gold en pub escence (Fig 2).
Head: Eyes moder ate in size. Transverse, triangu lar hea d (Fig 4) widest just beh ind eyes. Ver tex and occiput uniformly setifer ous with thick, blun t, ere ct gold en setae, and shorter, sharpe r pub escence. Margin s of larg e lateral
cavities for antenn al insertion and maxillary palp retraction carinate; interior s of cavities glab rous (Fig 5). Neck app roxima tely 0.4x hea d width between eyes, shining and with sparse, very short dar k setae on dor sal side; glab rous
and with finger-prin t-like (“str igate”) microsculp tur atio n on ventral side. Fourth segments of maxillary palp i (Fig 5) den sely covered in short gold en setae. Antenn ae (Fig 3) pigmen ted similarly to tibia and very elon gate,
app roxima tely 2x pro notum leng th. Antenn omere I conical, widest in basal half and equ al in leng th to III+IV combined. Latero dorsal margin with short arcuate carina extending to one-qua rte r antenn omere leng th. Latera l face
glab rous in basal half. With circular apical notch to per mit gen icula tion with II; II small and cylin drical, app roxima tely 0.6x the leng th of III; III cylin drical-obconical, equ al in leng th to IV; IV cylin drical, twice as long as wide; V slightly
shorter and nar rower than IV; V–VIII cylin drical-obconical, becoming gra dually shorter apically, so that segment V is almost 2x long er than wide and VIII is as only slightly long er than wide; IX–X much larg er, IX almost as long as
VI–VIII combined; X slightly long er than VII+VIII combined. Both IX and X cylin drical-obconical, apical margin s somewhat sloping interior ly due to slight leng the ning of exterior antenn omere face rela tive to interior face.
Antenn omere XI long est, twice the leng th of X; exterior face shallowly and evenly convex, interior face weakly concave before ben ding obtusely to form conical ape x. Severa l long sensory setae on apical third (Fig 3).
Thorax: Pro notum (Fig 4) obcord ate, margin s smooth, lacking crenula tion s or other pro tub erances. Uniformly setifer ous and pub escent. Pro sternu m with lateral long itud inal carinae abr uptly ben ding dor sally on rea chin g base (Fig
2). Region between carinae with red uce d setatio n and pub escence rela tive to lateral reg ions, and with small transverse pro jection situ ate d medially, anterio r to pro coxae. Region between carinae pro jecting sharply in basolatera l
por tion s to receive pro coxae. Mesoster num with setifer ous median mesoster nal foveae (MMSF) and lateral mesocoxa l fovea (LMCF). Region anterio r to mesocoxa e formed into a shield-shaped plate with carinate margin s. Anterio r
margin of metaster num carinate aro und mesocoxa e. Convex metaster num with median declivity adja cen t to metacoxa l pro jections. Metaster num uniformly covered with yellow pub escence of intermedia te leng th. Median declivity
somewhat less pub escent. Latera l metaster nal fovea small and setifer ous. Posterior margin of metaster num bow shaped (Fig 2); pro jection between metacoxa e with small medial inde nta tion.
Abdomen: Tergites str ongly convex with visib le tergite 1 (IV) sloping to abd omen base. Visible tergite 2 (V) bro adest, slightly bro ader than 1 (IV), with segments 3–5 (VI–VIII) evenly nar rowing. Tergite 4 (VII) long est, app roxima tely
1.5x tergite 3 (VI). Bro ad par ate rgites on segments 1–3 (IV–VI); par ate rgite margin s of segment 4 converging apically to create a triangu lar par ate rgite. Anterio r edg es of abd ominal tergites with nar row ban d of black pigmen t.
Remainder of tergite red dish bro wn; intertergital membran e yellow with latticed microsculp tur e. Base of visib le tergite 1 (IV) with short, blun t tubercles, situ ate d halfway between midline and lateral margin. First visib le ste rnite (IV)
medially acuminate in anterio r half, pro jecting ventrally between metacoxa e. Last visib le segment (6; VIII) with median declivity. Sternite 7 (XI) interna lised. Pub escence on ste rnites 2–6 (IV–VIII) becoming finer and sparser toward
midline (Fig 2).
Elytra: Blun t setae on elytra somewhat long er and slightly thicker than on other par ts of bod y. Apicolatera l ang les of elytra with margin s weakly excised (Fig 6).
Legs: Coxae contiguous. Mesocoxa e with pro ximodistal carina alon g posterior face. Metacoxa e glab rous except for pub escence on interna l face and aro und pro jection to trochanter. Apices of metacoxa e pro duced into flat, blun t
spines that extend posteriorly to half trochanter leng th (Fig 7). Metatrochanters with small rho mb oid-shaped tubercles on exterior face (Fig 7). Femora bro wnish red , covered with thick, blun t gold en setae. Tibia somewhat flatten ed
in pro ximal half, carinate alon g anterio r edg e to half-tibia leng th. Tibia lighter in colour than femora, yellowish bro wn, with similar but shorter setae. Tarsi nar row and long er than half tibial leng th; also yellowish bro wn, with fine,
sharp, aciculate setae. Pro tar sus with bifid anterio r claw (Fig 8).
Aedeagus: Asymmetric, bro ad, lacking par ameres (Fig 9 and 10). Wide, glob ose basal bulb with asymmetric left and righ t apical pro jections. An asymmetric, apically-truncate scle rotised stylus emerg es from with in the basal bulb.
Biological and collec tion inf ormat ion. The single specimen of J. towai was collecte d in a colony of Phe idole xanthogaster Wilson und er a log. The ants were app arently una war e of the bee tle, which was was found dee p inside
the nest. This suggests that J. towai is a true myrmeco phile, but information abo ut its biolo gy and beh avio ur are una vaila ble at this time. It has no clear myrmeco philous ada ptio ns, so may belo ng to the “ob ligate syn oekete” class.
2.1 Taxonomy
Jubogaster towai

Parker & Maruyama 2013

2.1 Taxonomy
Jubogaster towai
2.1 Taxonomy
2.1 Taxonomy
Jubogaster sp.
2.1 Taxonomy Batriscydmaenus tishechkini

Parker and Owens (2018)

Col. Bull.
2.1 Taxonomy
2.1 Taxonomy Hamotus heidiae

Parker et al (2024) Insectes Sociaux

2.1 Taxonomy

Acromyrmex histrix
2.1 Taxonomy Hamotus heidiae

Parker et al (2024) Insectes Sociaux

2.1 Homology

We can describe and catalogue organisms but….

….how do we infer evolutionary relationships between species?

Precondition for understanding how these organisms evolved

An organism’s phenotype decomposes into “characters”

(so too does an organism’s genome)

2.1 Homology

Hamotus heidiae Batriscydmaenus tisheckini

2.1 Homology

Hamotus heidiae Batriscydmaenus tisheckini

Antenna, present Ocular canthus, present Tarsus, 3-segmented

Antenna, 11-segmented Tarsus, with 2 claws

2.1 Homology

Hamotus heidiae Batriscydmaenus tisheckini

Homologous characters
2.1 Homology
Homologous characters:
Features shared by organisms due to common ancestry

Homologous

A basis for inferring evolutionary relationships

2.1 Homology
Homologous characters:
Features shared by organisms due to common ancestry

Homologous
2.1 Homology
Homologous characters:
Features shared by organisms due to common ancestry
2.3 Making trees: cladistics
Ernst Haeckel’s ‘Trees of Life’
2.3 Making trees: cladistics

ANIMALS
PLANTS

PROTISTS

FUNGI
BACTERIA
ARCHAEA
2.3 Making trees: cladistics

Phylogeny “reconstruction”
Objectively inferring evolutionary relationships using character data

Willi Hennig (1913-1976) An organism’s traits can be “coded” qualitatively

Discretized as Zeros and Ones:

0 (Character Absent)

1 (Character present)

2 (Character present, in different form)

Organisms differ in their

“character states”
2.3 Making trees: cladistics

Phylogeny “reconstruction”
Objectively inferring evolutionary relationships using character data

Willi Hennig (1913-1976)

METHOD: “Cladistics”

“States” of different characters scored

for different species, creating a character matrix:
Characters:
Taxa: 1 2 3 4 5 6 7 8 9 10
Species A 0 1 1 1 1 1 0 1 0 1
Species B 1 0 1 0 0 0 1 0 1 0
Species C 1 0 1 0 1 0 0 0 0 1
2.3 Making trees: cladistics

1 2 3 4 5 6 7 8 9 10
Species A 0111110101
Species B 1010001010
Species C 1010100001
Species D 0000000001

A priori, we cannot assume to ?

know the direction of evolution
(the “polarity of character state
change”) 0 1
2.3 Making trees: cladistics

But….in a phylogeny, we are

making explicit statements about
the polarity of character state
0 1 changes
0 1

We know the
common ancestor is
at this node.
0 1
0 1
Its character states are
phylogenetically primitive, ancestral
or “plesiomorphic” (Hennig, 1950)

We can there infer character state

changes across the tree with reference to it
2.3 Making trees: cladistics

How can we get to this point when

all we have is a character matrix of
extant species?
0 1
1 2 3 4 5 6 7 8 9 10
0 1 Species A 0111110101
Species B 1010001010
Species C 1010100001
Species D 0000000001
We know the
common ancestor is
at this node.
Its character states are
phylogenetically primitive, ancestral
or “plesiomorphic” (Hennig, 1950)

We can there infer character state

changes across the tree with reference to it
2.3 Making trees: cladistics

Cladistic
step 1:

These are all the possible fully resolved topologies

(i.e. no polytomies), onto which character state
changes can be mapped, without assuming
anything about the direction of change

Cladistic step 2: maps character state

changes onto all possible trees *
2.3 Making trees: cladistics
2.3 Making trees: cladistics
2.3 Making trees: cladistics

Cladistic step 3: invoke the principle of maximum parsimony

Occam’s Razor: the tree topology that requires the smallest number of
character state changes is the correct tree
(most assumption-free)
2.3 Making trees: cladistics

Shortest tree
or
“most
parsimonious”
How can we
infer polarity,
and resolve
relationships?
Tree lengths:
2.3 Making trees: cladistics

A species that we know, a priori, sits phylogenetically outside

of our clade of interest (= the “ingroup”)

Beetles
(Coleoptera)
“Ingroup”
The “root” *

Connects a
* Ascalaphid
(Neuroptera)
clade to the Outgroup
rest of the tree of life

Earliest split on the tree

2.3 Making trees: cladistics

A species that we know, a priori, sits phylogenetically outside

of our clade of interest (= the “ingroup”)

Beetles
(Coleoptera)
“Ingroup”
The “root”

Ascalaphid
Connects a (Neuroptera)
clade to the Outgroup
rest of the tree of life

“Rooting the tree” via outgroup

comparison
2.3 Making trees: cladistics
2.3 Making trees: cladistics

Rooting the tree => character state polarization

2.3 Making trees: cladistics

Shared, DERIVED (= non-primitive) character

AKA a “Synapomorphy” (Hennig, 1950)
0→1

Rooting the tree => character state polarization

2.3 Making trees: cladistics

Unique, DERIVED (= non-primitive) character

AKA an “Autapomorphy” (Hennig, 1950)

0→1

Rooting the tree => character state polarization

2.3 Making trees: cladistics

*A fundamental problem in phylogenetics:

With more taxa, the number of possible trees increases dramatically

No. No. possible

taxa unrooted trees
2 1
3 1
4 3
5 15
6 105
7 945
8 10,395
9 135,135
10 2,027,025
20 8,200,794,532,637,891,559,000!!!!!!!!

Mapping all character state changes to all possible trees is computationally

impossible for large numbers of taxa
2.3 Making trees: cladistics

Branch swapping: an ‘heuristic’ (quick and dirty) algorithm:

2.4 Molecular Phylogenetics
2.4 Molecular Phylogenetics
2.4 Molecular Phylogenetics
2.4 Molecular Phylogenetics
2.4 Molecular Phylogenetics

Only four possible nucleotides…

When DNA substitution rates are high, the probability of two lineages
independently evolving the same nucleotide at the same site increases…..

Erroneously interprets this similarity as a synapomorphy!!

Homoplasy (convergent substitutions at the same site)

Parsimony (cladistics) cannot distinguish homoplasious

changes from true, shared derived characters

Species with genes that possess:

> Lots of rapidly evolving insertions and deletions
> Very A-T rich genes (e.g. mitochondrial genes, many
endosymbiotic bacteria)
can be erroneously pulled together “Long Branch Attraction”
2.4 Molecular Phylogenetics

Maximum Likelihood, Bayesian inference: widely used alternatives to parsimony

Calculate the likelihood (ML) or posterior probability (BI)

of a topology and set of BRANCH LENGTHS (length
corresponding to estimated amount of sequence
evolution)
Which set of branch lengths make the data most likely?
Which set of branch lengths has the highest probability
given the data?
2.5 The molecular phylogeny revolution

Classically held view of animal relationships based on morphology

2.5 The molecular phylogeny revolution

Redrawing the Animal Tree of Life: Molecular Phylogenetics

18s ribosomal RNA

Present in every eukaryotic genome

Conserved regions good for resolving

deep relationships in the animal phylogeny

Zhou et al (2014) Science

2.5 The molecular phylogeny revolution

Redrawing the Animal Tree of Life: Molecular Phylogenetics

18s ribosomal RNA

Present in every eukaryotic genome

Conserved regions good for resolving

deep relationships in the animal phylogeny

Zhou et al (2014) Science

Easy to amplify with PCR: primers work in
every species, and locus is tandemly
repeated in genomes (identical sequences
maintained via gene conversion)
2.5 The molecular phylogeny revolution

Redrawing the Animal Tree of Life: Molecular Phylogenetics

18s ribosomal RNA

2.5 The molecular phylogeny revolution

Redrawing the Animal Tree of Life: Molecular Phylogenetics

18s ribosomal RNA

2.5 The molecular phylogeny revolution

18s rRNA: all moulting animal phyla form a clade: the Ecdysozoa

Ecdysozoa

Aguinaldo et al, 1997, Nature

2.5 The molecular phylogeny revolution

Deuterostomia

Nematodes secondarily “simplified”

Relationships between
early branching clades
currently controversial

“Phylogenomics”
2.5 The molecular phylogeny revolution

Classical view: Sponges (Phylum Porifera)

are earliest diverging animals

No nervous system or muscles

No body axes
No germ layers
Few cell types
2.5 The molecular phylogeny revolution

Metazoa

Ryan et al (2017) Science

2.5 The molecular phylogeny revolution
2.5 The molecular phylogeny revolution

Body Axis

No Body Axis

Body Axis

Moroz et al (2017) Nature

2.5 The molecular phylogeny revolution

Simion et al (2017) Current Biology Whelan et al (2017) Nature Eco Evo

2.5 The molecular phylogeny revolution
The latest…..
Synteny: conserved patterns of gene order along chromosomes
2.5 The molecular phylogeny revolution
The latest…..
Synteny: conserved patterns of gene order along chromosomes

Schultz et al (2023) Nature

Bi1e Evolution of the Biosphere

Lecture 3: Evolutionary Processes

3.1 History of Evolutionary Thought

3.2 Scales of Evolutionary Change
3.3 Population Genetic Processes

Instructor: Joe Parker, PhD

Beckman Behavioral Biology Room 226
[email protected]