Nagarjun's blog: Untangling the Mammalian Tree Wars

Why the tree of mammals remains disputed — and what we’ve learned from decades of phylogenomics

Introduction

When we think of the mammalian family tree, we often imagine a tidy branching diagram: monotremes split off first, then marsupials, then placentals, which split into the familiar primates, rodents, carnivores, hoofed mammals, bats, etc. In reality, the deeper branches of this tree have been hotly contested for decades. Researchers have proposed multiple competing topologies for how major mammal groups (especially within placentals) relate to each other, the timing of divergences, and how to interpret conflicts among gene phylogenies. That’s what’s often referred to as the “mammalian tree wars.”

In this post I trace the major controversies: their historical roots, major competing hypotheses, how genome-scale data have changed the picture (but not resolved everything), the key conceptual challenges (e.g., incomplete lineage sorting, rapid radiations), and where things stand today. I highlight important taxa, landmark papers, and what the persistent disagreements tell us about evolutionary genomics.

A brief historical overview

Morphology and early molecular work

Traditionally, mammalian systematics was based on morphological characters — dental patterns, ear bones, skull morphology, etc. By the late 20th century, molecular sequence data (e.g., mitochondrial genes, a few nuclear markers) began to be used, and soon major surprises appeared. For example, rodent-lagomorph affinities, the surprising grouping of hedgehogs, the suggestion of African endemic lineages of placentals (Afrotheria) that had previously been hidden.

In the early 2000s, key molecular-phylogenetic studies such as Murphy et al. 2001 – Resolution of the Early Placental Mammal Radiation (Science) found strong support (with Bayesian methods) for novel groupings of placental mammals. PMC+2Annual Reviews+2

The first major controversies: root of placental mammals

One of the earliest “wars” was about the root of the placental mammals: what is the first branch among the three major superorders (or clades) of placentals? The three competing hypotheses were:

Xenarthra‐first: xenarthrans (armadillos, sloths, anteaters) diverged first, then rest of placentals.
Afrotheria‐first: Afrotheria (elephants, hyraxes, sea-cows, tenrecs, etc) diverged first.
Atlantogenata: a clade combining Afrotheria + Xenarthra sister to Boreoeutheria (the other placentals).

Different studies found support for each of these, depending on gene sampling, taxon sampling, and methods. For instance, a critical review by Tarver et al. 2016 – Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference pointed out how challenging it is to infer this root reliably. OUP Academic+1

Divergence timing and post-KPg radiation

Another major piece of the war is “when” the major placental mammal lineages diversified. Did they radiate before or after the end-Cretaceous (KPg) extinction (~66 Ma)? Some studies (e.g., Meredith et al. 2011 – Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction on Mammal Diversification) suggested many ordinal groups started diverging in the Late Cretaceous; others argued for a rapid post-KPg explosion. The timing has strong implications for how we interpret the fossil record and ecological context of mammal diversification. PMC+1

Rapid radiations and short internodes

One thing many studies found: the branch lengths among the major clades are very short (in absolute time) meaning the divergences happened in quick succession. That rapid radiation means there is very little phylogenetic “signal” and lots of potential for conflicting gene trees. This is a major reason why “more data” has not simply solved the tree.

Key competing hypotheses and major taxa

Placental mammal major clades

A convenient summary: Most analyses now accept three big clades within placentals:

Afrotheria — African-origin mammals like elephants (Proboscidea), hyraxes (Hyracoidea), sirenians (sea cows), tenrecs and golden moles (Afrosoricida), elephant-shrews (Macroscelidea).
Xenarthra — armadillos, sloths, anteaters (South American origin).
Boreoeutheria — the rest, typically split into Euarchontoglires (primates, rodents, lagomorphs) and Laurasiatheria (carnivores, bats, perissodactyls/odd-toed ungulates, cetartiodactyls/hoofed mammals).

The root question is: which branch came off first, and what is the sister group relationship among them?

Hypothesis 1: Xenarthra -first

Some early and morphological/molecular studies suggested Xenarthra as the basal branch. That means Xenarthra diverged, then the remaining placentals split into Afrotheria + Boreoeutheria.

Hypothesis 2: Afrotheria-first

Other studies placed Afrotheria first, meaning the “African” mammals are basal, with xenarthrans and boreoeutherians later.

Hypothesis 3: Atlantogenata (Afrotheria + Xenarthra) sister to Boreoeutheria

This is now often considered the leading hypothesis: Afrotheria and Xenarthra form a clade (Atlantogenata), which is sister to Boreoeutheria. Some analyses support this strongly. OUP Academic+1

Divergence of Laurasiatheria and Euarchontoglires within Boreoeutheria

Even within Boreoeutheria, relationships have been contested. For example, the placement of bats, the relationships of perissodactyls (horses, rhinos) vs. cetartiodactyls (cows, pigs, whales), and how early diversifications proceeded.

Landmark papers and turning-points

Murphy et al. (2001, Science): “Resolution of the early placental mammal radiation using Bayesian phylogenetics.” One of the first large molecular datasets to propose novel placental relationships. BMC Ecology
Hallström & Janke (2008, BMC Evol Biol): used genome data to resolve many inter-ordinal relationships in placentals. Annual Reviews+1
McCormack et al. (2012, Genome Res): used ultraconserved elements (UCEs) to provide a larger genomic marker set for mammal sequence capture. PMC
Romiguier et al. (2013, Mol Biol Evol): “Less is more in mammalian phylogenomics: AT-rich genes minimise tree conflicts…” showing that gene choice matters a lot. OUP Academic
Liu et al. (2017, PNAS): “Genomic evidence reveals a radiation of placental mammals uninterrupted by the KPg boundary.” Suggests a somewhat earlier diversification than a pure post-KPg scenario. PNAS
Tarver et al. (2016, Genome Biol Evol): “The interrelationships of placental mammals and the limits of phylogenetic inference.” A sober survey of how hard this is. OUP Academic
More recently, reviews such as Springer et al. 2021 – Phylogenomics and the Genetic Architecture of the Placental Mammal Radiation have summarised the state of the field. Annual Reviews

Conceptual challenges: why the wars persist

Rapid divergences produce short internodes

When many lineages diverge in rapid succession, the period between splits is short. That means less time for unique mutations to accumulate, making the phylogenetic signal weak and gene tree discordance high. This is especially relevant for early placental divergences.

Incomplete lineage sorting (ILS)

Because ancestral populations may be large and polymorphic, different genes can trace different paths of inheritance. A gene tree may not match the species tree (the actual organismal branching). With short internodes, ILS is especially problematic. Some studies (e.g., Scornavacca & Galtier 2017 – Incomplete lineage sorting in mammalian phylogenomics) document this in mammals. PMC

Model misspecification and compositional bias

Genes evolve under different rates, compositional biases (GC content), and substitution patterns. If models don’t handle these correctly, you can get artefactual relationships. For example, Romiguier et al. (2013) found that AT-rich genes gave fewer conflicts. OUP Academic

Gene choice, taxon sampling, missing data

More data isn’t automatically better. Poorly sampled taxa or genes with lots of missing data can mislead. The choice of orthologs (single-copy vs duplicated) matters. And as Romiguier et al. show, fewer—but better—included genes may give better results.

Reticulate evolution, introgression, gene flow

Although major mammalian divergences probably don’t involve rampant hybridisation (as in some plants), there is still possibility of gene flow or incomplete reproductive isolation really early on, which can leave confusing signals.

Fossil calibration and timing issues

Part of the conflict isn’t just who is sister to whom, but when. Dating divergences relies on fossils, molecular clocks, and substitution-rate models. Divergence estimates for placentals swing widely depending on calibration choices. arXiv

Rooting the tree and outgroup choice

Especially for ancient splits, where you root the tree and how you treat the outgroup (e.g., marsupials, monotremes) matters. Mis‐rooting can flip major relationships.

What has genome-scale data solved, and what remains unresolved

Progress made

Many of the “easy” nodes are now well-supported. The monophyly of Afrotheria, Xenarthra, Boreoeutheria is widely accepted. PMC+1
Better resolution for many inter-ordinal relationships within Euarchontoglires and Laurasiatheria.
Encourage use of UCEs and large marker sets (McCormack et al. 2012) has improved marker availability.
Increasing use of coalescent‐aware methods (species tree estimation) to cope with gene tree heterogeneity.

Persistent issues

The exact root of the placental mammals still sees competing support sets (Afrotheria first vs Atlantogenata vs Xenarthra first).
The timing of diversification remains debated: many analyses find divergences pre-KPg; others support post-KPg rapid radiation. Liu et al. (2017) suggest the radiation was uninterrupted by the KPg boundary. PNAS
Some “hard” nodes within Laurasiatheria and within Euarchontoglires still lack consensus.
The magnitude of ILS and potential gene-flow has been underappreciated, meaning that even large datasets can produce strongly supported but conflicting trees (see Tarver et al. 2016). OUP Academic
Model adequacy: some large datasets are still being analysed with models that may not fit the data well.
Gene tree conflict: even in well-sampled data, concordance factors (genes or sites supporting a branch) may be low, meaning high bootstrap support is not always trustworthy.

The current consensus (such as it is)

Although not everything is settled, many analysts now favour the following view:

The first split in placentals is between Boreoeutheria and Atlantogenata (Afrotheria + Xenarthra).
Afrotheria and Xenarthra together form Atlantogenata.
Boreoeutheria then splits into Euarchontoglires and Laurasiatheria.
The diversification of major placental lineages is close to the KPg boundary (~66 Ma), although the exact timing is unresolved.

But even this may change with better sampling, better fossil calibration, and better models.

Why these “wars” matter

You might ask: “Does it matter if we swap the order of Afrotheria vs Xenarthra first?” Yes — it matters for many reasons:

Biogeography & palaeontology: If Afrotheria is basal, then African origin for many placentals is emphasised; if Xenarthra is basal, then South-American origins become more important.
Comparative genomics: Understanding which lineages diverged when helps interpret gene family expansions, genome duplications, adaptation and regulatory evolution.
Molecular rate inference and divergence time estimation: Root placement and branch ordering affect rate estimates, which in turn influence how we interpret macroevolution.
Trait evolution: If major clades diverged in particular sequences, trait states (e.g., sensory, metabolic, developmental) get different ancestral reconstructions.
Methodological implications: These mammalian tree wars are a case‐study in how phylogenetics works (and fails) in the era of big genomic data—ILS, rapid radiations, model misspecification.

Major taxa to watch and why

Elephants (Proboscidea), Sirenians, Tenrecs: key members of Afrotheria, so their genome placements matter for the “Afrotheria first” hypothesis.
Armadillos, Sloths, Anteaters (Xenarthra): similarly critical for rooting placentals.
Primates + Rodents + Lagomorphs (Euarchontoglires) vs Carnivores + Bats + Perissodactyls + Cetartiodactyls (Laurasiatheria): the interplay between these two large clades within Boreoeutheria holds many secrets about mammalian adaptation and diversification.
Whales & Hippos (Cetartiodactyla): their placement influences how we think about rapid adaptation, aquatic transitions, and gene family evolution in mammals.
Marsupials + Monotremes: Though the main wars focus on placentals, how we position non-placentals as outgroups (and how we root the mammal tree) affects the entire topology.

Lessons learned from the mammalian tree wars

More data is necessary but not sufficient. As Romiguier et al. (2013) found, gene selection matters: fewer, better genes might yield a more reliable tree than thousands of poorly chosen loci. OUP Academic
Coalescent methods matter. Accounting for gene tree heterogeneity (e.g., via ASTRAL, SVDquartets) is now standard.
Model fit is crucial. Even large datasets can give misleading trees if models are inadequate. Tarver et al. (2016) emphasise this. OUP Academic
Taxon sampling still matters. Some nodes remain uncertain simply because of poor sampling of lineages (especially extinct ones).
Conflict is informative. Rather than “ignoring” conflicting gene trees, current best practice is to explore what conflicts tell us about early speciation, hybridisation, or biases.
Integration of fossil, genomic and morphological data remains key. Relaxed molecular clock studies, fossil calibrations, and morphological traits all play a role; divergence timing remains one of the more contentious aspects.
Transparency, reproducibility, and metadata matter. Many papers now include concordance factors, gene tree summaries, and exploratory analyses of bias (e.g., site composition), which is good practice emerging from the mammalian wars.

Where next?

The mammalian tree wars are not over yet. Several frontiers remain:

Better genome assemblies: For many taxa (especially non-model ones) the sequences are still fragmented, misassembled, or poorly annotated. The era of high‐quality reference genomes across all mammalian orders will help.
Expanded taxon sampling (especially extinct): Incorporating fossil taxa (via ancient DNA or morphological placement) can help constrain divergence timing and rooting.
New marker types: Ultraconserved elements (UCEs), retroposons/retrotransposon insertions, rare genomic changes (RGCs) are being used to complement classical sequence alignments. For example McCormack et al. (2012) used UCEs. PMC
Network approaches: As some speciation events may involve reticulation (hybridisation, introgression), purely tree-based models may not suffice. This may become more relevant in mammals than previously thought.
Improved models: Models that can better handle compositional bias, heterotachy (rate variation across time), partitioning, incomplete lineage sorting, and gene duplication/loss will produce more reliable results.
Better chronological frameworks: Precise divergence time estimates need not only molecular clocks but better fossil calibration and model integration. A recent paper by Foley et al. (2023) suggests new timescales. Science
Trait‐genome‐phylogeny integration: Linking phylogeny to genome architecture, adaptive gene families, ecology, and morphology will enrich our understanding of mammalian evolution beyond just “who is related to whom”.

Conclusion

The saga of the mammalian tree wars reminds us that even with genomes, phylogenetics remains hard. Rapid ancient radiations, conflicting gene trees, model issues, and incomplete sampling mean that resolving even well-studied groups like mammals challenges our methods and assumptions.

Yet enormous progress has been made: broad clades are stable, many inter-relationships clearer, and the debates are now about the finer branches rather than wholesale restructuring. The “wars” haven’t disappeared—they’ve matured into rigorous scientific discourse about method, data quality, and inference limits rather than wholesale explosions of contradictory trees.

For evolutionary genomics, the mammalian tree wars provide a case study in how to do phylogenomics (and how not to). They underscore that data, method, biology, and interpretation must all align.

If you’re working on a mammalian phylogeny — or any deep phylogenetic question — remember: assembling thousands of genes is just the beginning. The real challenge lies in interrogating tree confidence, exploring conflict, and aligning genomic inference with biological reality.

Nagarjun's blog

Sunday, December 21, 2025

Untangling the Mammalian Tree Wars