Early Diversification Research Articles

Phylogenomics reveals a new generic delimitation of Asian Millettia, with reinstatements of Pongamia and Otosema (Fabaceae: Millettieae)

The generic relationships within the core Millettieae have not been well resolved to date. Millettia is considered one of the most problematic genera to classify within the core Millettieae, with approximately 150 species found in Asia and Africa. Recent molecular evidence has indicated that Millettia is highly polyphyletic. In this study, we utilized plastomes and single-copy nuclear genes from genome skimming sequencing to reconstruct the generic relationships and estimate the divergence time for the core Millettieae, focusing on the Asian species of Millettia. Our results revealed a broader circumscription of the core Millettieae with the inclusion of the Phaseoleae subtribe Ophrestiinae, consisting of 7 clades and 14 subclades within two main groups (canavanine and non-canavanine). The Asian species of Millettia were grouped into three distinct, well-supported subclades, leading us to propose a much narrower generic concept of Millettia, along with the reinstatements of the genera Pongamia and Otosema. Millettia s.str. was restricted to include only five species. Pongamia was recognized as a medium-sized genus that includes Fordia and Ibatiria, with approximately 58 species. Otosema, usually treated as a subgenus or section of Millettia, was resurrected as a distinct genus with three species. Our findings also indicated that the sampled African Millettia species belong to three subclades distinct from the Asian Millettia subclades, warranting further investigation in future studies. The dating result showed that the early rapid diversification of the core Millettieae during the Mid-Miocene Climatic Optimum involved several major problematic genera, including Derris s.l., Lonchocarpus s.l., and Millettia s.l., which may explain why these plant groups are difficult to classify. These results offer new insights into the phylogeny and taxonomy of the core Millettieae.

A nuclear phylogenomic tree of grasses (Poaceae) recovers current classification despite gene tree incongruence.

Grasses (Poaceae) comprise c. 11 800 species and are central to human livelihoods and terrestrial ecosystems. Knowing their relationships and evolutionary history is key to comparative research and crop breeding. Advances in genome-scale sequencing allow for increased breadth and depth of phylogenomic analyses, making it possible to infer a new reference species tree of the family. We inferred a comprehensive species tree of grasses by combining new and published sequences for 331 nuclear genes from genome, transcriptome, target enrichment and shotgun data. Our 1153-tip tree covers 79% of grass genera (including 21 genera sequenced for the first time) and all but two small tribes. We compared it to a newly inferred 910-tip plastome tree. We recovered most of the tribes and subfamilies previously established, despite pervasive incongruence among nuclear gene trees. The early diversification of the PACMAD clade could represent a hard polytomy. Gene tree-species tree reconciliation suggests that reticulation events occurred repeatedly. Nuclear-plastome incongruence is rare, with very few cases of supported conflict. We provide a robust framework for the grass tree of life to support research on grass evolution, including modes of reticulation, and genetic diversity for sustainable agriculture.

Comprehensive phylogenomic analysis of Zika virus: Insights into its origin, past evolutionary dynamics, and global spread

BackgroundZika virus (ZIKV), a Flaviviridae family member, has been linked to severe neurological disorders. Despite detailed studies on recent outbreaks, the early evolutionary history of ZIKV remains partially unclear. This study elucidates ZIKV origin and evolutionary dynamics, focusing on recombination events, early lineage diversification, and virus spread across continents. MethodsWe assessed recombination using multiple methods. We conducted Bayesian phylogenetic analyses to understand the evolutionary relationships and timing of key diversification events. Model selection was carried out to determine the most appropriate evolutionary model for our dataset. ResultsOur phylogenies revealed recent recombination between Singaporean and African lineages, indicating the co-circulation of diverse lineages during outbreaks. Thailand was identified as a crucial hub in the spread across Asia. The phylogenetic analysis suggests that the ZIKV lineage dates back to the eleventh century, with the first significant diversification occurring in the nineteenth century. The timing of the re-introduction of the Asian lineage into Africa and the delay between probable introduction and outbreak onset were also determined. ConclusionsThis study provides novel insights into ZIKV's origin and early evolutionary dynamics, highlighting Thailand's role in the spread of the virus in Asia and recent recombination events between distant lineages. These findings emphasize the need for continuous surveillance and a better understanding of ZIKV biology to forecast and mitigate future outbreaks.

The most detailed anatomical reconstruction of a Mesozoic coelacanth.

Although the split of coelacanths from other sarcopterygians is ancient, around 420 million years ago, the taxic diversity and the morphological disparity of the clade have remained relatively low, with a few exceptions. This supposedly slow evolutionary pace has earned the extant coelacanth Latimeria the nickname "living fossil". This status generated much interest in both extinct and extant coelacanths leading to the production of numerous anatomical studies. However, detailed descriptions of extinct taxa are made difficult due to the quality of the fossil material which generally prevents fine comparisons with the extant Latimeria. Here we describe a new genus and species of coelacanth, Graulia branchiodonta gen. et sp. nov. from the Middle Triassic of Eastern France, based on microtomographical imaging using synchrotron radiation. Through exquisite 3D preservation of the specimens, we reconstructed the skeletal anatomy of this new species at an unprecedented level of detail for an extinct coelacanth, and barely achieved for the extant Latimeria. In particular, we identified a well-developed trilobed ossified lung whose function is still uncertain. The skeletal anatomy of G. branchiodonta displays the general Bauplan of Mesozoic coelacanths and a phylogenetic analysis resolved it as a basal Mawsoniidae, shedding light on the early diversification of one of the two major lineages of Mesozoic coelacanths. However, despite its exquisite preservation, G. branchiodonta carries a weak phylogenetic signal, highlighting that the sudden radiation of coelacanths in the Early and Middle Triassic makes it currently difficult to detect synapomorphies and resolve phylogenetic interrelationships among coelacanths in the aftermath of the great Permo-Triassic biodiversity crisis.

A new leaf inhabiting ascomycete from the Jurassic (ca 170 Mya) of Yorkshire, UK, and insights into the appearance and diversification of filamentous Ascomycota

Leaf-associated fungi, the fungi that depend on leaves to sporulate, have a rich Cenozoic record, however their earlier diversity is poorly characterized. Here we describe Harristroma eboracense gen. et sp. nov., a Middle Jurassic leaf-associated fungus colonizing the leaf cuticle of Nilssonia tenuicaulis (cycadophyte). To place our newly described species into a picture of the diversification of Mesozoic fungi, we reassess fossils with leaf-associated stromata in the context of fungal molecular phylogeny. Being melanized, with radiate stromata, and on leaves, H. eboracense and other fossils from the Jurassic and earlier periods are probably related to filamentous Ascomycota in the superclass Leotiomyceta. Characters needed for further resolution of leaf-associated fungal biology and classification, such as the presence of an ostiole for spore discharge and appressoria for entry into leaf tissue first appear in the Mesozoic fossil record. Among Early Cretaceous fossils, Spataporthe taylorii represents the oldest unambiguous evidence of perithecial Sordariomycetes while Protographum luttrellii and Bleximothyrium ostiolatum are the oldest Dothideomycetes thyriothecia. Environmental observations show that broad leaved gymnosperms (especially cycadophytes) growing in warm temperate wet forests might have been the first environment for the radiation of Leotiomyceta.

Origin and early diversification of a high Andean rove-beetle clade: Corisantis gen. nov., phylogeny, and historical biogeography

A new genus, Corisantisgen. nov., within the Andean clade (AC) of the rove-beetle subtribe Philonthina, is described and illustrated, including 14 species. This new genus comprises six valid species formerly assigned to Belonuchus Nordmann (B. candens (Erichson, 1840) and B. pulchripennisBernhauer, 1908) and Philonthus (Ph. auripennis Bernhauer, 1916, Ph. caliensis Bernhauer, 1916, Ph. excellens Bernhauer, 1916, and Ph. whymperiSharp, 1891), along with nine newly described species: C. ancashensissp. nov., C. bongarensissp. nov., C. cajamarcanussp. nov., C. columbiensissp. nov., C. ecuatoriensissp. nov., C. grandissp. nov., C. levissp. nov., C. magdalensissp. nov., and C. napoensissp. nov. The four species originally classified under Philonthus are reassigned to Corisantis with the following new combinations: C. auripennis (Bernhauer, 1916) comb. nov., C. caliensis (Bernhauer, 1916) comb. nov., C. excellens (Bernhauer, 1916) comb. nov., and C. whymperi (Sharp, 1891) comb. nov. Additionally, Belonuchus pulchripennis is synonymized under Belonuchus candens (= B. pulchripennissyn. nov.), which is also transferred to Corisantis as C. candens (Erichson, 1840) comb. nov. Lectotypes are designated for B. pulchripennisBernhauer (1908), Philonthus candensErichson (1840) and Philonthus whymperiSharp (1891). This study provides diagnoses, redescriptions or descriptions, illustrations, a distribution map, and an identification key for the species of Corisantis. Phylogenetic analyses, employing three methodologies—Maximum Parsimony, Maximum Likelihood, and Bayesian Inference—consistently support the monophyly of Corisantis and confirm its sister-group relationship with Leptopeltoides Chani-Posse and Asenjo, with both genera being sister to Leptopeltus Bernhauer. Additionally, biogeographical analyses using two methodologies—BBM (Bayesian Binary MCMC) and S-DIVA (Statistical Dispersal-Vicariance Analysis)—suggest that the South American Transition Zone was the center of origin and early diversification for these three genera.

Discovery of new brown lacewings from the mid-Cretaceous Kachin amber highlights the Cretaceous diversity of Hemerobiidae (Insecta: Neuroptera)

Two new genera and two new species of the lacewing family Hemerobiidae, Mischemerobia yumini Chen, Zhuo & Liu gen. et sp. nov. and Pararchaeomegaloma suzheni Chen, Zhuo & Liu gen. et sp. nov., are described from the mid-Cretaceous Kachin amber in northern Myanmar. Mischemerobia Chen, Zhuo & Liu gen. nov. differs from the other genera by the complex configuration of forewing recurrent humeral veinlet, the presence of two forewing ORBs, and the forewing MP distally fused with CuA. Pararchaeomegaloma Chen, Zhuo & Liu gen. nov. can be distinguished from the other genera by the presence of only one forewing ORB, with posterior most branch deeply forked, and the forewing MP forked near wing margin. Our finding provides new evidence for understanding the Cretaceous diversity and early diversification of brown lacewings.

Ancient large-scale gene duplications and diversification in bryophytes illuminate the plant terrestrialization.

Large-scale gene duplications (LSGDs) are crucial for evolutionary adaptation and recurrent in vascular plants. However, the role of ancient LSGDs in the terrestrialization and diversification of bryophytes, the second most species-rich group of land plants, remains largely elusive due to limited sampling in bryophytes. Employing the most extensive nuclear gene dataset in bryophytes to date, we reconstructed a time-calibrated phylogenetic tree from 209 species, covering virtually all key bryophyte lineages, for phylogenomic analyses of LSGDs and diversification. We newly identified two ancient LSGDs: one in the most recent common ancestor (MRCA) of extant bryophytes and another in the MRCA of the majority of Jungermanniales s.lato.Duplicated genes from these two LSGDs show significant enrichment in photosynthesis-related processes and structures. Rhizoid-responsive ROOTHAIR DEFECTIVE SIX-LIKE (RSL) genes from ancient LSGDs are present in rhizoidless bryophytes, challenging assumptions about rhizoid absence mechanisms. We highlighted four major diversification rate upshifts, two of which slightly postdated LSGDs, potentially linked to the flourishing of gymnosperms and angiosperms and explaining over 80% of bryophyte diversity. Our findings, supported by extensive bryophyte sampling, highlight the significance of LSGDs in the early terrestrialization and diversification of bryophytes, offering new insights into land plant evolution.

Phylogeny and biogeography support ancient vicariance and subsequent dispersal out of Africa in Palpimanidae spiders (Araneae)

Abstract The Palpimanidae are one of five extant Palpimanoidea families that occur mainly in South America and Africa, although there are lineages in Madagascar, islands of the Indian Ocean, and parts of Asia. Here we examine the role of plate tectonics in shaping the distribution of Palpimanidae. We perform molecular sequencing via target enrichment, which makes use of fragmented DNA, because most specimens are stored in natural history museum collections and were not properly preserved for molecular sequencing. We perform phylogenetic analysis, divergence dating, and ancestral range reconstructions to assess whether continental vicariance shaped the evolution of Palpimanidae. We also examine evolution of eye loss via ancestral character reconstruction. We report the first Palpimanidae phylogeny based on genomic data that samples the majority of Chediminae genera. Results suggest that Palpimanidae originated in the Triassic, with diversification spanning the Jurassic to the Cretaceous. Vicarance played a role in early diversification, with later range expansion out of Africa. Based on morphology and phylogenetic analysis, Sceliraptor is synonymized with Sarascelis, Sceliscelis is synonymized with Scelidocteus, and the new genus and species Sitamacho tao gen. nov., sp. nov. is described, with three species transferred from Hybosida.

A burrowing annelid from the early Cambrian.

Soft-bodied fossils of annelids from the Cambrian are relatively rare but provide vital insights into the early evolution and diversification of annelids. Here we describe a new annelid, Xiaoshibachaeta biodiversa gen. et sp. nov., from the early Cambrian (Stage 3) Xiaoshiba biota of Kunming, Yunnan Provence, China. This worm is obliquely oriented in the sediment, and is characteristic of a cephalic cage-like structure formed by the anteriorly directed parapodia and long chaetae of chaetiger 1, strongly suggesting an endobenthic lifestyle. This first report of an annelid worm from the Xiaoshiba biota provides the earliest known plausible evidence of burrowing behaviour in Annelida. Phylogenetic analyses recover X. biodiversa in the polytomy with other crown-group Annelida, indicating that the evolution of cephalic cage in Annelida is most likely convergent.

New specimens of Bunaia woodwardi Clarke, 1919 (Euchelicerata): a new member of Offacolidae providing insight supporting the Arachnomorpha.

The rapid early diversification of arthropods has made understanding internal relationships within the group fiendish. Particularly unresolved is the origin of Euchelicerata, a clade consisting of the Prosomapoda (comprising the extant Xiphosura and Arachnida and the extinct Chasmataspidida, Eurypterida and synziphosurines) and the extinct Offacolidae. Here we describe new material of the Silurian 'synziphosurine' Bunaia woodwardi Clarke, 1919 that reveals previously unknown features of its ventral anatomy: a pair of elongated chelicerae in the prosoma, followed posteriorly by five pairs of biramous appendages, a first pre-abdomen somite bearing a pair of paddle-like uniramous appendages (exopods) and a ventral pretelsonic process. Phylogenetic analyses retrieve B. woodwardi as a member of Offacolidae closely related to Setapedites abundantis from the Early Ordovician Fezouata Biota. An anatomical comparison of the pretelsonic process of B. woodwardi, also present in Setapedites, with the posterior trunk morphologies of other Offacolidae, Habeliida and Vicissicaudata, suggests a possible homologous appendicular origin. This proposed apomorphic character supports a monophyletic Arachnomorpha, formed of Vicissicaudata, Habeliida and Euchelicerata. The establishment of this new homology could help to clarify the highly enigmatic phylogeny at the base of the euchelicerates as well as the sequence of character acquisition during their early evolution.

The Bica São Tomé fossil site, Paraná Basin, Rio Grande do Sul, Brazil: A unique window to the dawn of the Mesozoic Era

The Early Triassic is pivotal for understanding the recovery and diversification of post-extinction biotas, marking the initial emergence or early diversification of many modern life forms. This phase holds dual significance as it establishes the groundwork for contemporary biodiversity evolution and provides crucial insights into managing present ecological challenges. Focused efforts on the Sanga do Cabral Formation in the Paraná Basin unveil a critical opportunity for studying Early Triassic vertebrates in South America, offering a unique perspective on Western Gondwana's biotic recovery after the End-Permian Mass Extinction. Here, we review the geology and fossil record of the most important fossiliferous outcrop of the Sanga do Cabral Formation, the Bica São Tomé Fossil Site. Prospections at the outcrop have already recovered over two hundred specimens, including holotypes and representative materials of important Early Triassic taxa. Our review aims to demonstrate the relevance of the site and highlight strategies for its preservation. The site includes an unusual representation of archosauromorphs, although its content is dominated by procolophonids. Among the known localities of the Sanga do Cabral Formation, the Bica São Tomé Fossil Site stands out for the unique presence of well-preserved specimens in articulation, such as the nearly complete skeleton of the archosauromorph Teyujagua paradoxa. Even so, most of the record is dominated by fragmentary and reworked specimens. The Bica São Tomé site stands as a beacon for understanding Lower Triassic ecosystems in Latin America, presenting an unparalleled opportunity for Mesozoic exploration in Brazil. The Sanga do Cabral Formation, with its wealth of fossil evidence, promises to enrich our understanding of the Early Triassic period and its significance in shaping modern biodiversity.

Plant species diversification in the Himalaya-Hengduan Mountains region: an example from an endemic lineage of Pedicularis (Orobanchaceae) in the role of floral specializations and rapid range expansions.

The c. 270 endemic species of Pedicularis in the Himalaya-Hengduan Mountains (HHM) region exhibit high diversity in geographic distribution, elevational range and floral morphology. Many of these, including the species with the longest corolla tubes and beaked galeas, are monophyletic and represent a putative in situ radiation. In this study, we focus on the representative Clade 3 within the HHM region. We integrate the plastid phylogeny of this clade with environmental data and species distributions to infer environmental correlates of species diversity. We estimate macroevolutionary rates and reconstructed ancestral states for geographic ranges and corolla traits, and analyse patterns of range overlap and niche evolution to assess drivers of diversification in the HHM region. Our results show that the region from northwest Yunnan to southwest Sichuan is the centre of diversity for this clade of Pedicularis. Rates of diversification are associated with precipitation and multiple environmental factors. Multiple range expansions from the Sanjiang (Three Parallel Rivers) region, followed by allopatric speciation across the HHM region, contributed to early rapid diversification. Corolla traits are not significantly associated with species diversification. This study highlights the importance of integrated evidence for understanding species diversification dynamics and contributes to our understanding of the origins of the remarkable richness of plant species in the HHM region.

Of flippers and wings: The locomotor environment as a driver of the evolution of forelimb morphological diversity in mammals

Abstract The early diversification of tetrapods into terrestrial environments involved adaptations of their locomotor apparatus that allowed for weight support and propulsion on heterogeneous surfaces. Many lineages subsequently returned to the water, while others conquered the aerial environment, further diversifying under the physical constraints of locomoting through continuous fluid media. While many studies have explored the relationship between locomotion in continuous fluids and body mass, none have focused on how continuous fluid media have impacted the macroevolutionary patterns of limb shape diversity. We investigated whether mammals that left terrestrial environments to use air and water as their main locomotor environment experienced constraints on the morphological evolution of their forelimb, assessing their degree of morphological disparity and convergence. We gathered a comprehensive sample of more than 800 species that cover the extant family‐level diversity of mammals, using linear measurements of the forelimb skeleton to determine its shape and size. Among mammals, fully aquatic groups have the most disparate forelimb shapes, possibly due to the many different functional roles performed by flippers or the relaxation of constraints on within‐flipper bone proportions. Air‐based locomotion, in contrast, is linked to restricted forelimb shape diversity. Bats and gliding mammals exhibit similar morphological patterns that have resulted in partial phenotypic convergence, mostly involving the elongation of the proximal forelimb segments. Thus, whereas aquatic locomotion drives forelimb shape diversification, aerial locomotion constrains forelimb diversity. These results demonstrate that locomotion in continuous fluid media can either facilitate or limit morphological diversity and more broadly that locomotor environments have fostered the morphological and functional evolution of mammalian forelimbs. Read the free Plain Language Summary for this article on the Journal blog.

A new South American archaic ungulate and new insight for the early diversification of the South American native ungulates

ABSTRACT Palaeogene South American faunas include enigmatic ungulates that cannot be classified unequivocally within any of the main South American (SA) Native Ungulates clades (Litopterna, Notoungulata, Astrapotheria, Pyrotheria and Xenungulata) because they retain plesiomorphic features, resembling Laurasian ‘archaic ungulates’ traditionally classified within the order ‘Condylarthra’. Most SA ‘condylarths’ are known by partial dental series and isolated teeth and unassociated postcranial remains, hampering comparisons with better-known ungulates. Here, we describe a nearly complete skull and associated mandible of an SA ‘condylarth’, Talquinodus puertai gen. et sp. nov., preserving most of the dentition and basicranium, derived from middle Eocene rocks of the Sarmiento Formation at Central Patagonia. Talquinodus shows a combination of plesiomorphic traits (complete dentition with bunolophodont cheek teeth, ring like ectotympanic, retention of stapedial system, etc.), combined with some autapomorphies, as the reduction of the m3 talonid. Our phylogenetic analyses support consistently that Talquinodus belongs to the SA radiation of Euungulata along with Litopterna, Notoungulata and Astrapotheria. However, the internal relationships could not be resolved unambiguously: Talquinodus could be a didolodontid related to the origin of Litopterna, or could be part of a separate radiation of South American archaic ungulates, along Depaulacoutoia, Lamegoia and Escribania, with no descendants in post-Eocene faunas.

Cretaceous amber inclusions illuminate the evolutionary origin of tardigrades

Tardigrades are a diverse phylum of microscopic invertebrates widely known for their extreme survival capabilities. Molecular clocks suggest that tardigrades diverged from other panarthropods before the Cambrian, but their fossil record is extremely sparse. Only the fossil tardigrades Milnesium swolenskyi (Late Cretaceous) and Paradoryphoribius chronocaribbeus (Miocene) have resolved taxonomic positions, restricting the availability of calibration points for estimating for the origin of this phylum. Here, we revise two crown-group tardigrades from Canadian Cretaceous-aged amber using confocal fluorescence microscopy, revealing critical morphological characters that resolve their taxonomic positions. Formal morphological redescription of Beorn leggi reveals that it features Hypsibius-type claws. We also describe Aerobius dactylus gen. et sp. nov. based on its unique combination of claw characters. Phylogenetic analyses indicate that Beo. leggi and Aer. dactylus belong to the eutardigrade superfamily Hypsibioidea, adding a critical fossil calibration point to investigate tardigrade origins. Our molecular clock estimates suggest an early Paleozoic diversification of crown-group Tardigrada and highlight the importance of Beo. leggi as a calibration point that directly impacts estimates of shallow nodes. Our results suggest that independent terrestrialization of eutardigrades and heterotardigrades occurred around the end-Carboniferous and Lower Jurassic, respectively. These estimates also provide minimum ages for convergent acquisition of cryptobiosis.

The early sport specialization paradox: an argument for early sport diversification in female athletes.

The early sport specialization paradox: an argument for early sport diversification in female athletes.

They all floated in the cretaceous: new rebbachisaurid (Sauropoda, Diplodocoidea) with a highly pneumatized skeleton from the Upper Cretaceous (lower Cenomanian) of Patagonia, Argentina

ABSTRACT Rebbachisaurids are a group of basal diplodocoid sauropods that diversified primarily in Gondwana between the early Lower Cretaceous and the early Upper Cretaceous. Their phylogenetic relationships are still under debate given the fragmentary and incomplete nature of its remains. Here, we provide a detailed description of the postcranial remains of Campananeyen fragilissimus gen. et sp. nov. from the Candeleros Formation (lower Cenomanian) of Neuquén Province, Argentina. Campananeyen presents notable features that allow it to be recognised as a new species by the presence of an underdeveloped crista prootica, paraoccipital process internally hollow and a fuse dorsal alar arm of the ilium. The phylogenetic analysis recovered this taxon as a basal rebbachisaurid closely related to Zapalasaurus, Sidersaura and the specimen from La Amarga Formation MACN-Pv-N 35. The new rebbachisaurid is recovered as the sister taxon of Sidersaura due the presence of procoelous posterior caudal vertebrae and dorsoventrally flattened posterior caudal centra. C. fragilissimus presents an extreme pneumatization of the sacral region with an autapomorphic dorsal alar arm of the sacral transverse processes. Finally, the phylogenetic analysis supports a South American origin for Rebbachisauridae and an early diversification to Africa and Europe by the Barremian-Aptian as previously suggested.

Early Diversification of Membrane Intrinsic Proteins (MIPs) in Eukaryotes.

Membrane intrinsic proteins (MIPs), including aquaporins (AQPs) and aquaglyceroporins (GLPs), form an ancient family of transporters for water and small solutes across biological membranes. The evolutionary history and functions of MIPs have been extensively studied in vertebrates and land plants, but their widespread presence across the eukaryotic tree of life suggests both a more complex evolutionary history and a broader set of functions than previously thought. That said, the early evolution of MIPs remains obscure. The presence of one GLP and four AQP clades across both bacteria and archaea suggests that the first eukaryotes could have possessed up to five MIPs. Here, we report on a previously unknown richness in MIP diversity across all major eukaryotic lineages, including unicellular eukaryotes, which make up the bulk of eukaryotic diversity. Three MIP clades have likely deep evolutionary origins, dating back to the last eukaryotic common ancestor (LECA), and support the presence of a complex MIP repertoire in early eukaryotes. Overall, our findings highlight the growing complexity of the reconstructed LECA genome: the dynamic evolutionary history of MIPs was set in motion when eukaryotes were in their infancy followed by radiative bursts across all main eukaryotic lineages.

Complex but Clear Allopolyploid Pattern of Subtribe Tussilagininae (Asteraceae: Senecioneae) Revealed by Robust Phylogenomic Evidence, with Development of a Novel Homeolog-Sorting Pipeline.

Polyploidy is a significant mechanism in eukaryotic evolution and is particularly prevalent in the plant kingdom. However, our knowledge about this phenomenon and its effects on evolution remains limited. A major obstacle to the study of polyploidy is the great difficulty in untangling the origins of allopolyploids. Due to the drastic genome changes and the erosion of allopolyploidy signals caused by the combined effects of hybridization and complex post-polyploid diploidization processes, resolving the origins of allopolyploids has long been a challenging task. Here we revisit this issue with the interesting case of subtribe Tussilagininae (Asteraceae: Senecioneae) and by developing HomeoSorter, a new pipeline for network inferences by phasing homeologs to parental subgenomes. The pipeline is based on the basic idea of a previous study but with major changes to address the scaling problem and implement some new functions. With simulated data, we demonstrate that HomeoSorter works efficiently on genome-scale data and has high accuracy in identifying polyploid patterns and assigning homeologs. Using HomeoSorter, the maximum pseudo-likelihood model of Phylonet, and genome-scale data, we further address the complex origin of Tussilagininae, a speciose group (ca. 45 genera and 710 species) characterized by having high base chromosome numbers (mainly x = 30, 40). In particular, the inferred patterns are strongly supported by the chromosomal evidence. Tussilagininae is revealed to comprise two large groups with successive allopolyploid origins: Tussilagininae s.s. (mainly x = 30) and the Gynoxyoid group (x = 40). Two allopolyploidy events first give rise to Tussilagininae s.s., with the first event occurring between the ancestor of subtribe Senecioninae (x = 10) and a lineage (highly probably with x = 10) related to the Brachyglottis alliance, and the resulting hybrid lineage crossing with the ancestor of Chersodoma (x = 10) and leading to Tussilagininae s.s. Then, after early diversification, the Central American group (mainly x = 30) of Tussilagininae s.s., is involved in a third allopolyploidy event with, again, the Chersodoma lineage and produces the Gynoxyoid group. Our study highlights the value of HomeoSorter and the homeolog-sorting approach in polyploid phylogenetics. With rich species diversity and clear evolutionary patterns, Tussilagininae s.s. and the Gynoxyoid group are also excellent models for future investigations of polyploidy.