Ancient Divergence Research Articles

Insights into the Genetic Connectivity and Climate-Driven Northward Range Expansion of Turbo sazae (Gastropoda: Turbinidae) Along the Eastern Coast of Korea.

Turbo sazae, a commercially and ecologically significant marine gastropod traditionally found in Jeju Island and the southern coast of Korea, is experiencing a reported northward expansion into the East Sea, likely influenced by rising seawater temperatures. This study provides preliminary genetic insights into the genetic structure and connectivity of T. sazae populations between Jeju and the East Sea using mitochondrial COI sequences. Samples from 6 geographically distinct locations were analyzed, with three cloned replicates generated to enhance sequence reliability. Genetic diversity, haplotype distribution, and population differentiation were then assessed. Our analysis reveals potential genetic connectivity between Jeju and East Sea populations, possibly driven by larval dispersal via the Kuroshio and Tsushima Currents, highlighted by the predominance of shared haplotype EJ1 (60.0% in Jeju, 50.0% in East Sea). Bayesian phylogenetic analysis estimated the time to the most recent common ancestor (MRCA) between Jeju and East Sea populations at approximately 9.7 to 23.3 million years ago, indicating ancient divergence rather than very recent separation. Pairwise FST values and AMOVA results showed generally low levels of genetic differentiation. Given the small sample sizes and use of a single mitochondrial marker, these findings should be interpreted cautiously as preliminary evidence. Nevertheless, this study highlights the need for continued genetic monitoring of T. sazae populations under climate-driven range shifts and provides a foundation for future research incorporating broader genomic approaches.

Ancient diversity of Triticum aestivum subspecies as source of novel loci for bread wheat improvement.

Ancient subspecies of hexaploid wheat, not yet subjected to intensive selection, harbor potentially valuable alternative genetic variability for the genetic improvement of modern cultivated bread wheat. To investigate these hitherto unexplored resources, we established a panel, currently unique, consisting of 190 accessions of Triticum aestivum belonging to five different neglected subspecies, compactum, sphaerococcum, macha, spelta, and vavilovii, with few aestivum references. The panel was genotyped through the iSelect Illumina arrays (20K and 25K) and phenotyped for 25 traits related to phenology, morphology, yield, and physiology for 4 years under field conditions. We found wide variability for all traits analyzed, both within and among subspecies, demonstrating the richness contained therein. Through a genome-wide association study (GWAS), we identified a total of 126 marker-trait associations (MTAs), including 4 for years, 58 for morphological traits, 39 related to yield, and 25 for physiological traits, some of them confirming loci previously published and others being novel. Fourteen MTAs were associated with multiple traits. Among them, one on chromosome 2D at 360.2 Mb was associated with spike density, length, and shape, and thus is of particular interest because it may underlie the compactum (C) gene, until now considered difficult to clone because of its centromeric position. The physical distance defined by this MTA is considerably smaller (1.7 Mb) than what is reported so far in the literature, paving the way toward physical mapping of the C gene. A potential candidate gene has been identified for the trait grain number per spike. This is TraesCS6A03G0476500, coding for a monosaccharide-sensing protein 2, located on chromosome 6A at 233 Mb and identified through an MTA that segregates exclusively in compactum accessions. The results obtained confirm the remarkable potential present in the panel of wheat subspecies analyzed in this study, which, being characterized by a very short linkage disequilibrium (LD) decay, allowed the definition of rather narrow ranges around key traits, such as those related to yield, providing new perspectives on transferring genes across subspecies for wheat improvement.

Rapidly evolved genomic regions shape individual language abilities in present-day humans.

1 Minor genetic changes have produced profound differences in cognitive abilities between humans and our closest relatives, particularly in language. Despite decades of research, ranging from single-gene studies to broader evolutionary analyses[1, 2, 3, 4, 5], key questions about the genomic foundations of human language have persisted, including which sequences are involved, how they evolved, and whether similar changes occur in other vocal learning species. Here we provide the first evidence directly linking rapidly evolved genomic regions to language abilities in contemporary humans. Through extensive analysis of 65 million years of evolutionary events in over 30,000 individuals, we demonstrate that Human Ancestor Quickly Evolved Regions (HAQERs)[5] - sequences that rapidly accumulated mutations after the human-chimpanzee split - specifically influence language but not general cognition. These regions evolved to shape language development by altering binding of Forkhead domain transcription factors, including FOXP2 . Strikingly, language-associated HAQER variants show higher prevalence in Neanderthals than modern humans, have been stable throughout recent human history, and show evidence of convergent evolution across other mammalian vocal learners. An unexpected pattern of balancing selection acting on these apparently beneficial alleles is explained by their pleiotropic effects on prenatal brain development contributing to birth complications, reflecting an evolutionary trade-off between language capability and reproductive fitness. By developing the Evolution Stratified-Polygenic Score analysis, we show that language capabilities likely emerged before the human-Neanderthal split - far earlier than previously thought[3, 6, 7]. Our findings establish the first direct link between ancient genomic divergence and present-day variation in language abilities, while revealing how evolutionary constraints continue to shape human cognitive development.

Seascape Genomics of Elacatinus punctiulatus (Ginsburg, 1938): Understanding the Historical and Contemporary Drivers of Population Structure in the Gulf of California.

The genomic diversity and population structure of marine species represents a complex mosaic shaped by historical and contemporary environmental seascape features that maintain or alter it over time. The Gulf of California (GC) is an interior sea with a dynamic history during its formation and a contemporary environmental and oceanographic complexity; hence, it is a suitable system to test the effect of historical and contemporary factors on genomic diversity in marine species. We investigated the genomic seascape of the redhead goby (Elacatinus puncticulatus; Ginsburg, 1938), a cryptobenthic marine fish, to gain insights into the historical and contemporary drivers shaping its population structure in the GC. A total of 4802 SNPs markers were analysed, with 3775 loci classified as neutral markers and 27 as outlier markers potentially under selection. Both markers demonstrated population structure, with the neutral markers showing two main groups corresponding to northern and southern locatities. The outlier markers identified an additional genetic group emerging in the central area of the sampled localities. Genetic differentiation between the North and South regions and historical demographic simulations was consistent with ancient divergence (1.04 Mya) and secondary contact (0.15 Mya). The genomic environmental association analysis revealed a possible adaptive scenario linked to ocean temperature. The study highlights the importance of historical events, contemporary environmental factors, and oceanographic circulation in shaping the genetic structure of E. puncticulatus populations in the GC.

Chromosome-level genome provides novel insights into the starch metabolism regulation and evolutionary history of Tetraselmis helgolandica.

Chromosome-level genome provides novel insights into the starch metabolism regulation and evolutionary history of Tetraselmis helgolandica.

Function and Evolution of the Plant MES Family of Methylesterases.

Land plant evolution has been marked by numerous genetic innovations, including novel catalytic reactions. Plants produce various carboxyl methyl esters using carboxylic acids as substrates, both of which are involved in diverse biological processes. The biosynthesis of methyl esters is catalyzed by SABATH methyltransferases, and understanding of this family has broadened in recent years. Meanwhile, the enzymes catalyzing demethylation-known as methylesterases (MESs)-have received less attention. Here, we present a comprehensive review of the plant MES family, focusing on known biochemical and biological functions, and evolution in the plant kingdom. Thirty-two MES genes have been biochemically characterized, with substrates including methyl esters of plant hormones and several other specialized metabolites. One characterized member demonstrates non-esterase activity, indicating functional diversity in this family. MES genes regulate biological processes, including biotic and abiotic defense, as well as germination and root development. While MES genes are absent in green algae, they are ubiquitous among the land plants analyzed. Extant MES genes belong to three groups of deep origin, implying ancient gene duplication and functional divergence. Two of these groups have yet to have any characterized members. Much remains to be uncovered about the enzymatic functions, biological roles, and evolution of the MES family.

Chromosome scale genome assembly and annotation of coconut cultivar Chowghat Green Dwarf

The high-quality genome of coconut (Cocos nucifera L.) is a crucial resource for enhancing agronomic traits and studying genome evolution within the Arecaceae family. We sequenced the Chowghat Green Dwarf cultivar, which is resistant to the root (wilt) disease, utilizing Illumina, PacBio, ONT, and Hi-C technologies to produce a chromosome-level genome of ~ 2.68 Gb with a scaffold N50 of 174 Mb; approximately 97% of the genome could be anchored to 16 pseudo-molecules (2.62 Gb). In total, 34,483 protein-coding genes were annotated; the BUSCO completeness score was 96.80%, while the k-mer completeness was ~ 87%. The assembled genome includes 2.19 Gb (81.64%) of repetitive sequences, with long terminal repeats (LTRs) constituting the most abundant class at 53.76%. Additionally, our analysis confirms two whole-genome duplication (WGD) events in the C. nucifera lineage. A genome-wide analysis of LTR insertion time revealed ancient divergence and proliferation of copia and gypsy elements. In addition, 1368 RGAs were discovered in the CGD genome. We also developed a web server ‘Kalpa Genome Resource’ (http://210.89.54.198:3000/), to manage and store a comprehensive array of genomic data, including genome sequences, genetic markers, structural and functional annotations like metabolic pathways, and transcriptomic profiles. The web server has an embedded genome browser to analyze and visualize the genome, its genomics elements, and transcriptome data. The in-built BLAST server allows sequence homology searches against genome, annotated transcriptome & proteome sequences. The genomic dataset and the database will support comparative genome analysis and can expedite genome-driven breeding and enhancement efforts for tapping genetic gains in coconut.

Revisiting the four Hexapoda classes: Protura as the sister group to all other hexapods

Insects represent the most diverse animal group, yet previous phylogenetic analyses based on morphological and molecular data have failed to agree on the evolutionary relationships of early insects and their six-legged relatives (together constituting the clade Hexapoda). In particular, the phylogenetic positions of the three early-diverging hexapod lineages-the coneheads (Protura), springtails (Collembola), and two-pronged bristletails (Diplura)-have been debated for over a century, with alternative topologies implying drastically different scenarios of the evolution of the insect body plan and hexapod terrestrialization. We addressed this issue by sampling all hexapod orders and experimenting with a broad range of across-site compositional heterogeneous models designed to tackle ancient divergences. Our analyses support Protura as the earliest-diverging hexapod lineage ("Protura-sister") and Collembola as a sister group to Diplura, a clade corresponding to the original composition of Entognatha, and characterized by the shared possession of internal muscles in the antennal flagellum. The previously recognized 'Elliplura' hypothesis is recovered only under the site-homogeneous substitution models with partial supermatrices. Our cross-validation analysis shows that the site-heterogeneous CAT-GTR model, which recovers "Protura-sister," fits significantly better than homogeneous models. Furthermore, the morphologically unusual Protura are also supported as the earliest-diverging hexapod lineage by other lines of evidence, such as mitogenomes, comparative embryology, and sperm morphology, which produced results similar to those in this study. Our backbone phylogeny of hexapods will facilitate the exploration of the underpinnings of hexapod terrestrialization and megadiversity.

A taxon-rich and genome-scale phylogeny of Opisthokonta.

Ancient divergences within Opisthokonta-a major lineage that includes organisms in the kingdoms Animalia, Fungi, and their unicellular relatives-remain contentious. To assess progress toward a genome-scale Opisthokonta phylogeny, we conducted the most taxon rich phylogenomic analysis using sets of genes inferred with different orthology inference methods and established the geological timeline of Opisthokonta diversification. We also conducted sensitivity analysis by subsampling genes or taxa from the full data matrix based on filtering criteria previously shown to improve phylogenomic inference. We found that approximately 85% of internal branches were congruent across data matrices and the approaches used. Notably, the use of different orthology inference methods was a substantial contributor to the observed incongruence: analyses using the same set of orthologs showed high congruence of 97% to 98%, whereas different sets of orthologs resulted in somewhat lower congruence (87% to 91%). Examination of unicellular Holozoa relationships suggests that the instability observed across varying gene sets may stem from weak phylogenetic signals. Our results provide a comprehensive Opisthokonta phylogenomic framework that will be useful for illuminating ancient evolutionary episodes concerning the origin and diversification of the 2 major eukaryotic kingdoms and emphasize the importance of investigating effects of orthology inference on phylogenetic analyses to resolve ancient divergences.

Earthworm (Oligochaeta, Lumbricidae) intraspecific genetic variation and polyploidy.

Earthworms are known for their intricate systematics and a diverse range of reproduction modes, including outcrossing, self-fertilization, parthenogenesis, and some other modes, which can occasionally coexist in a single species. Moreover, they exhibit considerable intraspecific karyotype diversity, with ploidy levels varying from di- to decaploid, as well as high genetic variation. In some cases, a single species may exhibit significant morphological variation, contain several races of different ploidy, and harbor multiple genetic lineages that display significant divergence in both nuclear and mitochondrial DNA. However, the relationship between ploidy races and genetic lineages in earthworms remains largely unexplored. To address this question, we conducted a comprehensive review of available data on earthworm genetic diversity and karyotypes. Our analysis revealed that in many cases, a single genetic lineage appears to encompass populations with different ploidy levels, indicating recent polyploidization. On the other hand, some other cases like Octolasion tyrtaeum and Dendrobaena schmidti/D. tellermanica demonstrate pronounced genetic boundaries between ploidy races, implying that they diverged long ago. Certain cases like the Eisenia nordenskioldi complex represent a complex picture with ancient divergence between lineages and both ancient and recent polyploidization. The comparison of phylogenetic and cytological data suggests that some ploidy races have arisen independently multiple times, which supports the early findings by T.S. Vsevolodova-Perel and T.V. Malinina. The key to such a complex picture is probably the plasticity of reproductive modes in earthworms, which encompass diverse modes of sexual and asexual reproduction; also, it has been demonstrated that even high-ploidy forms can retain amphimixis.

A passage through India: The biotic ferry model supports the build‐up of Indo‐Australian biodiversity of an ancient soil arthropod clade

AbstractAimScutigeromorpha is a globally distributed, ancient group of centipedes with at least 400 million years of evolutionary history. We assess the biogeographic history of the order, with a particular focus on the Peninsular Indian Plate (PIP), a Gondwanan fragment. We hypothesize that continental vicariance explains the disjunct distribution of extant scutigeromorphs, that PIP scutigeromorphs are of ancient Gondwanan origins, and that East Gondwana vicariance explains the diversification of the subfamily Thereuoneminae into its Asian and Australian clades.LocationGlobal.TaxaCentipedes, Scutigeromorpha.MethodsWe use a novel molecular dataset sampled across the PIP and a global sequence database representing the geographic distribution of all families and subfamilies. We employ molecular phylogenetic analyses on two mitochondrial and three nuclear markers, molecular species delimitation and ancestral range estimation to reconstruct biogeographic history.ResultsAncestral scutigeromorphs were likely widely distributed across Gondwana and diverged prior to any continental vicariance. Their subsequent biogeography is shaped by continental vicariance, long‐distance dispersal and jump dispersal, indicating an ability to colonize areas far from their ancestral range. The PIP emerged as the ancestral range of Thereuoneminae, which started diversifying during the Cretaceous Period. Subsequent in‐situ diversification within the PIP and dispersals into Asia, Australia and the Pacific Islands best explained the extant distribution of Thereuoneminae, more so than East Gondwana vicariance.Main ConclusionsThe in‐situ diversification of PIP species and their ancient divergence suggest they represent Gondwanan relicts in a landmass whose biota is primarily dispersal‐driven. A single dispersal event from the PIP generated most of the extant diversity in Australia, another Gondwanan fragment. Furthermore, the discovery of 11 putative species from the PIP and the Andaman Islands, five times more than was known, highlights the Wallacean and Linnean shortfalls in tropical Asia.

Decoding the Chloroplast Genome of Tetrastigma (Vitaceae): Variations and Phylogenetic Selection Insights.

Tetrastigma (Vitaceae) is known for its ornamental, medicinal, and ecological significance. However, the structural and variational characteristics of the Tetrastigma chloroplast genome and their impact on phylogenetic relationships remain underexplored. This study utilized bioinformatics methods to assemble and annotate the chloroplast genomes of 10 Tetrastigma species and compare them with five previously sequenced species. This study analyzed gene composition, simple sequence repeats, and codon usage patterns, revealing a high A/T content, uniquely identified pentanucleotide repeats in five species and several preferred codons. In addition, comparative analyses were conducted of the chloroplast genomes of 15 Tetrastigma species, examining their structural differences and identifying polymorphic hotspots (rps16, rps16-trnQ, trnS, trnD, psbC-trnS-psbZ, accD-psaI, psbE-petL-petG, etc.) suitable for DNA marker development. Furthermore, phylogenetic and selective pressure analyses were performed based on the chloroplast genomes of these 15 Tetrastigma species, validating and elucidating intra-genus relationships within Tetrastigma. Futhermore, several genes under positive selection, such as atpF and accD, were identified, shedding light on the adaptive evolution of Tetrastigma. Utilizing 40 Vitaceae species, the divergence time of Tetrastigma was estimated, clarifying the evolutionary relationships within Tetrastigma relative to other genera. The analysis revealed diverse divergences of Tetrastigma in the Miocene and Pliocene, with possible ancient divergence events before the Eocene. Furthermore, family-level selective pressure analysis identified key features distinguishing Tetrastigma from other genera, showing a higher degree of purifying selection. This research enriches the chloroplast genome data for Tetrastigma and offers new insights into species identification, phylogenetic analysis, and adaptive evolution, enhancing our understanding of the genetic diversity and evolutionary history of these species.

Genomic SNPs resolve the phylogeny of an ancient amphibian island radiation from the Seychelles

Unusually for oceanic islands, the granitic Seychelles host multiple lineages of endemic amphibians. This includes an ancient (likely ca. 60 million years) radiation of eight caecilian species, most of which occur on multiple islands.These caecilians have a complicated taxonomic history and their phylogenetic inter-species relationships have been difficult to resolve. Double-digest RAD sequencing (ddRADseq) has been applied extensively to phylogeography and increasingly to phylogenetics but its utility for resolving ancient divergences is less well established. To address this, we applied ddRADseq to generate a genome-wide SNP panel for phylogenomic analyses of the Seychelles caecilians, whose phylogeny has so far not been satisfactorily resolved with traditional DNA markers. Based on 129,154 SNPs, we resolved deep and shallow splits, with strong support. Our findings demonstrate the capability of genome-wide SNPs for evolutionary inference at multiple taxonomic levels and support the recently proposed synonymy of Grandisonia Taylor, 1968 with Hypogeophis Peters, 1879. We revealed three clades of Hypogeophis (large-, medium- and short-bodied) and identify a single origin of the diminutive, stocky-bodied and pointy-snouted phenotype.

Chromosomal inversions from an initial ecotypic divergence drive a gradual repeated radiation of Galápagos beetles.

Island faunas exhibit some of the most iconic examples where similar forms repeatedly evolve within different islands. Yet, whether these deterministic evolutionary trajectories within islands are driven by an initial, singular divergence and the subsequent exchange of individuals and adaptive genetic variation between islands remains unclear. Here, we study a gradual, repeated evolution of low-dispersive highland ecotypes from a dispersive lowland ecotype of Calosoma beetles along the island progression of the Galápagos. We show that repeated highland adaptation involved selection on multiple shared alleles within extensive chromosomal inversions that originated from an initial adaptation event on the oldest island. These highland inversions first spread through dispersal of highland individuals. Subsequent admixture with the lowland ecotype resulted in polymorphic dispersive populations from which the highland populations evolved on the youngest islands. Our findings emphasize the significance of an ancient divergence in driving repeated evolution and highlight how a mixed contribution of inter-island colonization and within-island evolution can shape parallel species communities.

Exploring hidden diversity: Molecular insights into the Leporinus species of the rivers of the Brazilian states of Maranhão and Piauí.

The present study delved into the world of hidden diversity by examining specimens identified as Leporinus piau from the river basins of the northern Brazilian states of Maranhão and Piauí. Using genetic analyses that combined data from three mitochondrial markers and one nuclear marker, the study identified two well-supported groups, reinforcing the findings of previous publications. The first group, found in samples from the Itapecuru, Mearim, Turiaçu, and Pericumã basins, in Maranhão, appears to represent a relatively ancient diversification and the possibility of concealed cryptic diversity. The second group, comprising specimens from the Parnaíba (Piauí) and Mearim (Maranhão) basins, appears to have resulted from a more recent process of diversification and has a close relationship with Leporinus friderici from the type locality. Our findings not only confirm the existence of a complex scenario of cryptic diversity in the genus Leporinus from the study basins but also underscore the taxonomic inconsistencies within this group of fish. This study offers a comprehensive analysis of the species diversity of the Maranhão and Piauí basins, which are critical regions for the conservation of Amazonian fish, providing valuable insights for the sustainable management and conservation of these fish.

Unveiling ancient diversity of long-tailed wasps (Hymenoptera: Megalyridae): new taxa from Cretaceous Kachin and Taimyr ambers and their phylogenetic affinities

The Megalyridae are a small family of parasitoid wasps comprising eight extant genera (71 species) and six extinct genera (13 species). Here, we report eight new species from Late Cretaceous Kachin (Myanmar) and Taimyr (Russia) ambers; the family is recorded for the first time from the latter. †Cretolyra noijebumensisgen. et sp. nov., †Cretolyra shawigen. et sp. nov., †Genkyhag innebulagen. et sp. nov., †Megacoxa chandrahrasagen. et sp. nov., †Megacoxa janzenigen. et sp. nov., and †Megacoxa synchrotrongen. et sp. nov., are described from late Albian – early Cenomanian Kachin amber; †Kamyristi exfrigoregen. et sp. nov. and †Kamyristi yantardakhensisgen. et sp. nov. from Taimyr amber (Baikura, late Albian – early Cenomanian Ognevka Formation and Yantardakh, Santonian Kheta Formation, respectively). Phylogenetic analyses of the family are presented and the classification of the Megalyridae is revised accordingly. A new tribe, †Megalavinitrib. nov., is erected to accommodate †Cretolyragen. nov., †Genkyhaggen. nov., †Megacoxagen. nov. together with †Megalava Perrichot, 2009; †Megalavinitrib. nov. is characterized by the vein M fully pigmented and veins Rs+M and M+Cu aligned, the crenulate mesometapectal sulcus, and the pronotal spiracle not posteriorly surrounded by cuticle. This spiracular condition was previously only observed in †Megazar Perrichot, 2009, thus the subfamily †Megazarinae Perrichot, 2009 stat. nov. is proposed for the clade (†Megalavini + †Megazar), as sister to the remaining Megalyridae. The latter is defined as the Megalyrinae, with †Kamyristigen. nov. being retrieved as sister to all other genera except Rigel Shaw, 1987 under parsimony analyses. To align phylogeny with classification, three new tribes are erected (†Kamyristinitrib. nov., †Megallicinitrib. nov., and †Valaainitrib. nov.) and the †Cretodinapsini is synonymized under Megalyrini. A grouping [Rigel + Megalyridia] is supported under Bayesian analyses, which is the only specific conflict with the parsimony analyses, suggesting some degree of caution with respect to the internal relationships of the Megalyrinae. Finally, a revised key to the Megalyridae genera is provided.

A new neopasiphaeine bee associated with flowers of Loasaceae (Hymenoptera: Colletidae: Actenosigynes).

The genus Actenosigynes includes two species, A. fulvoniger (Michener, 1989) and A. mantiqueirensis Silveira, 2009, both oligolectic on flowers of Blumenbachia (Loasaceae) in southern Brazil. We describe a third species, Actenosigynes silveirai Siriani-Oliveira, sp. n., and provide additional evidence to the suspected narrow host-plant specificity between bees of this genus and Loasaceae. This new species was only recorded to collect resources on flowers of Aosa, a genus closely related to Blumenbachia in the subfamily Loasoideae. We illustrate female and male specimens of the three species to offer a complete summary of the morphological variation within this modestly sized genus of Neopasiphaeinae, including photographs of male genitalia and associated metasomal sterna. Moreover, we provide an identification key for the three species of Actenosigynes and the first phylogenetic and dating estimate for these taxa. The genus diversified in southern South America during the Miocene-Pliocene, following a more ancient divergence associated with the orogenic events that separated its sister-genus, Torocolletes, west of the Andes. We dedicate this newly described species to Fernando A. Silveira for his contributions to research on Brazilian bee taxonomy and biology.

Identification and cellular localization in Xenopus laevis photoreceptors of three Peripherin-2 family members, Prph2, Rom1 and Gp2l, which arose from gene duplication events in the common ancestors of jawed vertebrates

Identification and cellular localization in Xenopus laevis photoreceptors of three Peripherin-2 family members, Prph2, Rom1 and Gp2l, which arose from gene duplication events in the common ancestors of jawed vertebrates

The oldest fossil bird-like footprints from the upper Triassic of southern Africa.

Footprint morphology reflects the anatomy of the trackmaker's foot and is direct evidence for the animal's behaviour. Consequently, fossil tracks can be used to infer ancient diversity, ethology, and evolutionary trends. This is particularly useful for deep-time intervals during which the early history of an animal group is reliant upon limited fossil skeletal material. Fossil tracks of early birds and theropods, the co-existing dinosaurian ancestors of birds, co-occur in the rock record since the Early Cretaceous. However, the evolutionary transition from dinosaur to bird and the timing of the birds' origin are still contested. Skeletal remains of the basal-most birds Aurornis, Anchiornis, Archaeopteryx and Xiaotingia are Middle to Late Jurassic, while tracks with tentative bird affinities, attributed to dinosaurs, are known from as early as the Late Triassic. Here, we present numerous, well-provenanced, Late Triassic and Early Jurassic tridactyl tracks from southern Africa, with demonstrable bird-like affinities, predating basal bird body fossils by c. 60 million years.

Ancient diversity in host-parasite interaction genes in a model parasitic nematode

Host-parasite interactions exert strong selection pressures on the genomes of both host and parasite. These interactions can lead to negative frequency-dependent selection, a form of balancing selection that is hypothesised to explain the high levels of polymorphism seen in many host immune and parasite antigen loci. Here, we sequence the genomes of several individuals of Heligmosomoides bakeri, a model parasite of house mice, and Heligmosomoides polygyrus, a closely related parasite of wood mice. Although H. bakeri is commonly referred to as H. polygyrus in the literature, their genomes show levels of divergence that are consistent with at least a million years of independent evolution. The genomes of both species contain hyper-divergent haplotypes that are enriched for proteins that interact with the host immune response. Many of these haplotypes originated prior to the divergence between H. bakeri and H. polygyrus, suggesting that they have been maintained by long-term balancing selection. Together, our results suggest that the selection pressures exerted by the host immune response have played a key role in shaping patterns of genetic diversity in the genomes of parasitic nematodes.