Bat origins summarized on ResearchGate

Evidently
some paleo workers are not all that interested in using the tool of phylogenetic analysis to recover broad interrelationships among mammals and other vertebrate clades. Others keep waiting for transitional fossils to cross their desk. When workers do create cladograms, they tend to omit pertinent taxa. Such efforts too often result in left over enigmas and data vacuums.

This might be just fine because something, like a mystery to be solved, has to draw students into lecture halls and college bookstores.

Many former enigmas and vacuums already have been solved and filled by the large reptile tree (LRT, 2340 taxa) and large pterosaur tree (LPT 268 taxa) by simply testing more taxa.

The following brief manuscript with no figures was recently uploaded to ResearchGate.net so it would be accessible to others via their excellent index system. Since traditional publication in peer-reviewed journals is now blocked for yours truly, this available avenue has been taken as a detour.

If there’s a problem to be solved, roll up your sleeves and do something about it.

The origin of bats in phylogenetic analysis.
This is a preprint. Comments and collaboration offers are welcome.

Abstract
The origin of bats (clade Chiroptera) has remained elusive until now due to taxon exclusion. Bat fossil taxa capable of flapping flight extend to the early Eocene, 52mya. Earlier transitional fossils have not been described. Suprageneric molecular studies have not been helpful. Here a wide gamut phylogenetic trait-based analysis that tests the interrelationships of 2340 competing fossil and extant vertebrate genera recovers bats derived from the genus Microcebus, the smallest extant lemur, a previously overlooked taxon. 

Cladogram online here: https://reptileevolution.com/reptile-tree.htm

Introduction
Among vertebrates, only birds, pterosaurs and bats are/were able to fly. The origin of birds from Late Jurassic Solnhofen feathered theropods, like Archaeopteryx (Owen 1863), was proposed by Huxley in 1871, then resurrected by Ostrom in 1976, then gradually recognized by other paleontologists after the appearance of so many Early Cretaceous feathered theropod fossils from China in the 1990s. The origin of pterosaurs from Middle Triassic tiny tanystropheids, like Cosesaurus (Ellenberger and DeVillalta 1974), was proposed by Peters (1997, 2000a,b, 2002), then moved from archosauromorph prolacertiforms to a new clade of lepidosaurs derived from Huehuecuetzpalli by Peters 2007. The search for the mammal ancestors of bats was recently summarized by Sadier et al 2021, who wrote, “the lack of fossils capturing the transition from terrestrial mammal to volant chiropteran has obscured much of our understanding of bat evolution.” The phylogenetic origin of bats from the smallest extant primate, Microcebus, a previously overlooked outgroup taxon, is the subject of this paper. 

Flapping as a derived behavior
What all three flying vertebrate clades (birds, pterosaurs and bats) have in common is the ability to flap their forelimbs. This is an obvious change from the plesiomorphic left-right-left-right motion of quadrupedal forelimbs. In Solnhofen birds and pterosaur ancestors this change to flapping is signaled by the elongation of locked-down coracoids. This innovation prevented the plesiomorphic ventral sliding of the disc-like primitive coracoid along the lateral rim of the sternum. It also raised the shoulder glenoid, expanding the space for the ever-larger pectoral muscles essential for flapping. In this transition the scapula also became strap-like and located dorsally. Lacking a coracoid, bats substituted a longer, already locked-down clavicle. By contrast, Microcebus lacks elongate locked-down clavicles and does not attempt to flap. It retains the plesiomorphic condition for mammals.  That’s why it went unnoticed until now.

Obviously, flapping can only happen in bipeds. Basal birds, like Archaeopteryx, were obligate bipeds arising from obligate biped theropods with relatively shorter forelimbs. Basal pterosaurs, like Bergamodactylus, were obligate bipeds arising from obligate biped tiny tanystropheids, like Longisquama and Sharovipteryx. Middle Triassic Cosesaurus was a transitional biped. It had relatively shorter hindlimbs, like those of late-surviving Huehuecuetzpali. In the three non-volent Triassic pre-pterosaurs elongate, locked-down coracoids were present indicating the initiation of flapping. This behavior was likely used as a secondary sexual signal (Peters 2002, 2009) emhanced with various extradermal membranes. The hands and feet of Cosesaurus were matched to Early and Middle Triassic Rotodactylus tracks (Peters 2000a), which were sometimes quadrupedal, other times bipedal and some trackways show the transition. Basal bats (with a long tail) are inverted bipeds. That is, when not flying they typically hang from their feet. By contrast, some derived bats and derived wading pterosaurs became secondarily quadrupedal. In pterosaurs finger three creates a posterior impression in pterosaur trackways, indicating it was not plesiomorphcally quadrupedal. Microcebus is capable of 3m leaps through the air, but is quadrupedal and does not flap. That’s why it went unnoticed until now.

Feathers, fibers and membranes
For thrust and lift all three clades of flying vertebrates expand their forelimbs. Birds did so with extradermal wing feathers inherited from non-volant ancestors. Pterosaurs did so with extradermal trailing membranes embedded with fibers inherited from non-volant ancestors (Peters, 2000a, 2002, 2009). Bats did so with interdigital membranes retained from embryonic interdigital membranes. These expanded along with the hyper-elongation of the four lateral fingers. Microcebus does not have expanded forelimbs nor extradermal membranes. That’s why it went unnoticed until now.

Phylogeny
When paleontologists lack obvious transitional fossils and molecular studies are not helpful, the best recourse is to run a phylogenetic analysis that includes a wide gamut of fossil and extant taxa. More taxa minimize the possibility of taxon exclusion, a common problem in systematics. The large reptile tree (LRT) is an online cladogram that represents a wide gamut analysis that began in 2011 with 240 vertebrate taxa. In the last 15 years the LRT expanded its taxon list ten-fold. Given the present wide gamut of 600+ competing pre-mammal and mammal taxa, the LRT nests the bat clade, Chiroptera, within the clade Primates, derived from the smallest living primate, Microcebus. The extant, long-tailed genus, Tadarida is a basal bat in the LRT. 

A matrix of taxa and multi-state traits was compiled in Mesquite. The heuristic search option was used in PAUP. The cladogram was built over time in Adobe Illustrator. A jpeg and PDF file were generated from that. 

Colugos and tree shrews
In the LRT colugos are also primates, derived from lemurs close to Indri. Thus, colugos are not related to bats. Primates, carnivores and hoofed mammals evolved from Monodelphis domestica. Members of this first placental clade retained plesiomorphic canines. By contrast, tree shrews arose from a second origin of placental mammals derived from marsupial phalangers (Petaurus) and possums (Gymnobelideus and Dactylopsila). Earlier this clade lost plesiomorphic canines. Sometimes an anterior premolar took its place, the so-called double-rooted canine. Sometimes this tooth was also lost.

Phylogenetic miniaturization
In the LRT, Archaeopteryx was a phylogenetically miniaturized theropod dinosaur. In the LRT Cosesaurus, Sharovipteryx, Longisquama and Bergamodactylus were phylogenetically miniaturized tanystropheid lepidosaurs. In the LRT Microcebus was a phylogenetically miniaturized lemur and the long-tailed bat, Tadarida was even smaller. Precocious maturation over many generations is one cause of phylogenetic miniaturization.  

Genomics
Trait-based LRT results differ greatly from all genomic cladograms that comparatively test deep time molecules. As an example, the traditional genomic clades ‘Afrotheria’ and ‘Laurasiatheria’ are not recovered by the LRT. Reasons for this are not known and beyond the scope of this phenomic study. 

Comparative anatomy and behavior
Microcebus murinus (Miller 1777) is the extant gray mouse lemur, an omnivore restricted to the lower levels of dense tropical forests of Madagascar. As in bats, Microcebus is mostly insectivorous. It supplements its diet with occasional small tree reptiles and frogs, leaves, fruits and flowers. Individuals forage alone, but sleep in groups, sharing tree holes during the day, like some bats do. Atypical for primates, but typical for bats, Microcebus can enter a seasonal torpor and a daily torpor. Breeding is seasonal. Twin offspring are typical. Infants weigh from up to 7g and are carried in the mother’s mouth during transport, distinct from bats, which carry young on their chest. Gray mouse lemur offspring are independent after two months and can reproduce after one year with a typical lifespan of ten years. This is broadly similar to bats.

Microcebus has large eyes and large ears. Insects are captured on the ground with hands in the jungle leaf litter. Before descending on prey, the ear pinnae are directed to help pinpoint the precise location, as in bats. Vocalizations are complex and high-pitched (10 to 36 kHz), beyond the range of humans (up to 20kHz), as in bats.

Conclusions
In the present absence of fossils of transitional pre-bats, phylogenetic analysis nests bats with the small lemur primate, Microcebus, a previously overlooked candidate for bat ancestry. 

Supplementary materials
Matrices for ‘The ReptileEvolution.com Project’ can be downloaded at FigShare.com.

Citations
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Huxley TH 1871. Manual of the anatomy of vertebrate animals. London.
Ostrom J H 1976. Archaeopteryx and the origin of birds. Biological Journal of the Linnean Society. 8 (2):91–182.
Owen R 1863. On the Archaeopteryx von Meyer, with a description of the fossil remains of a long-tailed species from the lithographic stone of Solnhofen. Philosophical Transactions of the Royal Society, London 153: 33-47.
Peters 1997. A new phylogeny for the Pterosauria. Journal of Vertebrate Paleontology Abstracts of Papers. Fifty-seventh annual meeting. Chicago, Illinois.
Peters D 2000a. Description and Interpretation of Interphalangeal Lines in Tetrapods.  Ichnos 7:11-41.
Peters D 2000b. A Redescription of Four Prolacertiform Genera and Implications for Pterosaur Phylogenesis. Rivista Italiana di Paleontologia e Stratigrafia 106 (3): 293–336.
Peters D 2002. A New Model for the Evolution of the Pterosaur Wing – with a twist. Historical Biology 15: 277-301
Peters D 2007. The origin and radiation of the Pterosauria. In D. Hone ed. Flugsaurier. The Wellnhofer pterosaur meeting, Munich, Germany: 27.
Peters D 2009. A Reinterpretation of Pteroid Articulation in Pterosaurs – Short Communication. Journal of Vertebrate Paleontology 29(4):1327–1330.
Sadier A, Urban DJ, Anthwal N, Howenstine AO, Sinha I, Sears KE 2021. Making a bat: The developmental basis of bat evolution. Genet Mol Biol. 2021 Feb 8;43(1 Suppl 2):e20190146. doi: 10.1590/1678-4685-GMB-2019-0146. PMID: 33576369; PMCID: PMC7879332.
Simmons NB, Seymour KL, Habersetzer J, Gunnell GF 2008. Primitive Early Eocene bat from Wyoming and the evolution of flight and echolocation. Nature. 2008;451:818–821. doi: 10.1038/nature06549.

Source: https://pterosaurheresies.wordpress.com/2026/05/24/bat-origins-summarized-on-researchgate/