Ancestral Pattern Research Articles

Exploring the Influence of Neomorphic Gekkotan Paraphalanges on Limb Modularity and Integration.

Digital specializations of geckos are widely associated with their climbing abilities. A recurring feature that has independently emerged within the sister families Gekkonidae and Phyllodactylidae is the presence of neomorphic paraphalanges (PPEs), usually paired, paraxial skeletal structures lying adjacent to interphalangeal and metapodial-phalangeal joints. The incorporation of PPEs into gekkotan autopodia has the potential to modify the modularity and integration of the ancestral limb pattern by affecting information flow among skeletal limb parts. Here we explore the influence of PPEs on limb organization using anatomical networks. We modeled the fore- and hindlimbs in species ancestrally devoid of PPEs (Iguana iguana and Gekko gecko) and paraphalanx-bearing species (Hemidactylus mabouia and Uroplatus fimbriatus). To further clarify the impact of PPEs we also expunged PPEs from paraphalanx-bearing network models. We found that PPEs significantly increase modularity, giving rise to tightly integrated sub-modules along the digits, suggesting functional specialization. Species-specific singularities also emerged, such as the trade-off between the presence of PPEs favoring modularity (along the proximodistal axis) and the interdigital webbing favoring integration (across the lateromedial axis) in the limbs of U. fimbriatus. The PPEs are characterized by low connectivity compared with other skeletal elements; nevertheless, this varies based on their specific location and seemingly reflects developmental constraints. Our results also highlight the importance of the fifth metatarsal in generating a shift in lepidosaurian hindlimb polarity that contrasts with the more symmetrical bauplan of tetrapods. Our findings support extensive modification of the autopodial system in association with the addition of the neomorphic and intriguing PPEs.

The larval chondrocranium and its development in Smilisca phaeota with considerations of patterns characteristic for the chondrocranial development of Lalagobatrachia

Several studies describe the development of the chondrocranium of vertebrates. The details in these studies vary a lot, which makes it hard to compare developmental patterns and identify evolutionary trends. Therefore, we aim to close this gap for anurans, which is the largest order of amphibians. We present here a detailed description of the chondrocranium morphology and development of Smilisca phaeota, the New Granada cross-banded tree frog. The anatomy was described for the larvae at or older than Gossner stage 31 and before ossification starts. Following this, we describe the development of the chondrocranium from Gossner stages 19–26. Early in Gossner stage 19 no precursors of any cartilages are visible, while later in that stage the mesodermal Anlage of Meckel’s cartilage was observed. In the subsequent stages more and more mesodermal anlagen become identifiable, followed by chondrification, and final differentiation of the cartilage elements. We used serial sections to study all the developmental stages and additionally utilized cleared and stained specimens and CT scan data. The latter were also used for the 3D reconstruction of the chondrocranium. We previously studied several species and compared these developmental patterns with S. phaeota, revealing potentially characteristic patterns significant for Lalagobatrachia, a clade that includes over 7000 frog species. These include (1) the suprarostral alae develop before the suprarostral corpus, (2) the infrarostral cartilage chondrifies late, after the chondrification of ceratobranchial 1, and (3) the ceratohyal body is the first element to show chondrocytes and to chondrify. However, with only six species studied so far, our data only provide a basis for future studies and developing hypotheses about the ancestral developmental pattern in anurans.

The first mitogenome of the subfamily Stenoponiinae (Siphonaptera: Ctenophthalmidae) and implications for its phylogenetic position

Fleas are the most important insect vectors that parasitize warm-blooded animals and are known vectors of zoonotic pathogens. A recent study showed that Stenoponia polyspina parasitizing Eospalax baileyi in Zoige County have carried Bartonella spp. and Spotted fever group Rickettsia (SFGR). Accurate identification and differentiation of fleas are essential for prevention and control of zoonotic pathogens. To understand phylogenetic relationship of the subfamily Stenoponiinae, we described morphological characteristics of S. polyspina and sequenced its mitogenome with 14,933 bp in size and high A + T content (~ 79%). The S. polyspina mitogenome retained the ancestral pattern of mitochondrial gene arrangement of arthropods without rearrangement. The start codons of 13 protein-coding genes (PCGs) are traditional ATN and the stop codons are TAA or TAG. Anticodon loops of all tRNA genes were 7 bp except for trnL2 and trnD had anticodon loops with 9 bp and the abnormal anticodon loops may be associated with frameshifting mutation. Genetic distance and Ka/Ks ratios indicated that all 13 PCGs of S. polyspina were subjected to purifying selection, with cox1 at the slowest rate and atp8 at the fastest rate. The mitogenomes of 24 species representing 7 families in the order Siphonaptera were selected to reconstruct phylogenetic tree based on concatenated nucleotide sequences of two datasets (PCGRNA matrix and PCG12RNA matrix) using Bayesian inference (BI) and Maximum likelihood (ML) methods. Phylogenetic tree supported that the superfamilies Ceratophylloidea, Vermipsylloidea, Pulicoidea were monophyletic and the superfamily Hystrichopsylloidea was paraphyletic. The family Ctenophthalmidae was monophyletic in PCGRNA-ML (codon partition) and paraphyletic in the remain trees. S. polyspina belongs to the subfamily Stenoponiinae was closely more related to the subfamily Rhadinopsyllinae. This paper explored phylogenetic position of diverse clades within the order Siphonaptera based on morphological and mitogenome data of S. polyspina. Our research enriched NCBI database of the order Siphonaptera.

Macrovibrissae and microvibrissae inversion and lateralization in elephants.

Elephants are known for strongly lateralized trunk behaviors, but the mechanisms driving elephant lateralization are poorly understood. Here, we investigate features of elephant mouth organization that presumably promote lateralization. We find the lower jaw of elephants is of narrow width, but is rostrally strongly elongated even beyond the jaw bone. Elephant lip vibrissae become progressively longer rostrally. Thus, elephants have two lateral dense, short microvibrissae arrays and central, less dense long macrovibrissae. This is an inversion of the ancestral mammalian facial vibrissae pattern, where central, dense short microvibrissae are flanked by two lateral macrovibrissae arrays. Elephant microvibrissae have smaller follicles than macrovibrissae. Similar to trunk-tip vibrissae, elephant lip microvibrissae show laterally asymmetric abrasion. Observations on Asian zoo elephants indicate lateralized abrasion results from lateralized feeding. It appears that the ancestral mammalian mouth (upper and lower lips, incisors, frontal microvibrissae) is shaped by oral food apprehension. The elephant mouth organization radically changed, however, because trunk-mediated feeding replaced oral apprehension. Such elephant mouth changes include the upper lip-nose fusion to the trunk, the super-flexible elongated lower jaw, the loss of incisors, and lateral rather than frontal microvibrissae. Elephants' specialization for lateral food insertion is reflected by the reduction in the centering effects of oral food apprehension and lip vibrissae patterns.

Mitogenomic Insights into the Evolution, Divergence Time, and Ancestral Ranges of Coturnix Quails.

The Old-World quails, Coturnix coturnix (common quail) and Coturnix japonica (Japanese quail), are morphologically similar yet occupy distinct geographic ranges. This study aimed to elucidate their evolutionary trajectory and ancestral distribution patterns through a thorough analysis of their mitochondrial genomes. Mitogenomic analysis revealed high structural conservation, identical translational mechanisms, and similar evolutionary pressures in both species. Selection analysis revealed significant evidence of positive selection across the Coturnix lineage for the nad4 gene tree owing to environmental changes and acclimatization requirements during its evolutionary history. Divergence time estimations imply that diversification among Coturnix species occurred in the mid-Miocene (13.89 Ma), and their current distributions were primarily shaped by dispersal rather than global vicariance events. Phylogenetic analysis indicates a close relationship between C. coturnix and C. japonica, with divergence estimated at 2.25 Ma during the Pleistocene epoch. Ancestral range reconstructions indicate that the ancestors of the Coturnix clade were distributed over the Oriental region. C. coturnix subsequently dispersed to Eurasia and Africa, and C. japonica to eastern Asia. We hypothesize that the current geographic distributions of C. coturnix and C. japonica result from their unique dispersal strategies, developed to evade interspecific territoriality and influenced by the Tibetan Plateau's geographic constraints. This study advances our understanding of the biogeographic and evolutionary processes leading to the diversification of C. coturnix and C. japonica, laying important groundwork for further research on this genus.

Unraveling the phylogeny of Chaetopteridae (Annelida) through mitochondrial genome analysis

Mitochondrial genomes serve as valuable markers for phylogenetic and evolutionary studies across diverse invertebrate taxa, but their application within Annelida remains limited. In this study, we report the mitochondrial genomes of seven species from four genera of Chaetopteridae (Annelida), obtained by high-throughput sequencing. Phylogenetic analysis was performed using cox1, 18S, 28S and all mitochondrial genes. Our results reveal Chaetopterus and Mesochaetopterus as well-supported monophyletic sister clades, while Phyllochaetopterus and Spiochaetopterus appear paraphyletic, with species from both genera in a mixed clade sister to Chaetopterus + Mesochaetopterus. While mitochondrial gene orders remain conserved within Chaetopteridae, they appear substantially different from those of the ancestral patterns in Annelida. All 13 protein-coding genes found in Chaetopteridae evolved under strong purification selection, although Phyllochaetopterus exhibited the highest base-substitution rate for most of them, suggesting a more relaxed purified selection. Overall, our study provides molecular resources for phylogenetic studies of Chaetopteridae, highlighting the necessity for a comprehensive revision of the family, particularly dealing with the paraphyletic Phyllochaetopterus and Spiochaetopterus.

Evolutionary adaptations generally reverse phenotypic plasticity to restore ancestral phenotypes during new environment adaptation in cattle.

Phenotype plasticity and evolution adaptations are the two main ways in which allow populations to deal with environmental changes, but the potential relationship between them remains controversial. Using a reciprocal transplant approach with cattle adapted to the Tibetan Plateau and adjacent lowlands, we aim to investigate the relative contributions of evolutionary processes and phenotypic plasticity in driving both phenotypic and transcriptomic changes under natural conditions. We observed that while numerous genetic transcriptomic changes were evident during the forward adaptation to highland environments, plastic changes predominantly facilitate the transformation of transcriptomes into a preferred state when Tibetan cattle are reintroduced to lowland habitats. Genes with ancestral plasticity are generally reversed by evolutionary adaptations and show a closer expression level to the ancestral stage in evolved Tibetan cattle. A similar trend was also observed at the phenotypes level, with a majority of biochemical and hemorheology phenotypes showing a tendency to revert to their ancestral patterns, suggesting the restoration of ancestral expression levels is a widespread evolutionary trend during adaptation. The findings of our study contribute to the debate regarding the relative contributions of plasticity and genetic changes in mammal environment adaptation. Furthermore, we highlight that the restoration of ancestral phenotypes represents a general pattern in cattle new environment adaptation.

Evolution of Maternal Provisioning and Development in the Ophiuroidea: Egg Size, Larval Form and Parental Care.

The Ophiuroidea is the most speciose class of echinoderms and has the greatest diversity of larval forms, but we know less about the evolution of development (evo-devo) in this group than for the other echinoderm classes. As is typical of echinoderms, evo-devo in the Ophiuroidea resulted in the switch from production of small eggs and feeding (planktotrophic) larvae to large eggs and non-feeding (lecithotrophic) larvae. Parental care (ovoviviparity or viviparity/matrotrophy) is the most derived life history. Analysis of egg data for 140 species (excluding viviparity and facultative planktotrophy) indicated a bimodal distribution in egg volume corresponding to planktotrophy and lecithotrophy+ovoviviparity, with three significant egg size groups due to the very large eggs of the ovoviviparous species. The marked reduction in fecundity in species with extremely large eggs is exemplified by the ovoviviparous species. Egg size in the two species with facultative planktotrophy were intermediate with respect to the two modes. Identifying the ancestral larval life history pattern and the pathways in the switch from feeding to non-feeding larvae is complicated by the two patterns of metamorphosis seen in species with planktotrophic development: Type I (ophiopluteus only) and Type II (ophiopluteus+vitellaria larva). The variability in arm resorption at metamorphosis across ophiuroid families indicates that the Type I and II patterns may be two ends of a morphological continuum. This variability indicates ancestral morphological plasticity at metamorphosis followed by canalization in some taxa to the vitellaria as the metamorphic larva. Vestigial ophiopluteal traits in lecithotrophic ophioplutei and vitellaria indicate evolution from the ancestral (feeding larva) state. Parental care has evolved many times from an ancestor that had a planktonic ophiopluteus or vitellaria and is often associated with hermaphroditism and paedomorphosis. A secondary reduction in egg size occurred in the viviparous species.

Chromosomal organization of different repetitive sequences in four wasp species of the genus Trypoxylon Latreille (Hymenoptera: Crabronidae) and insights into the composition of wasp telomeres.

This study characterizes the chromosomal organization of DNA repetitive sequences and the karyotypic evolution in four representatives of the solitary wasp genus Trypoxylon using conventional and molecular cytogenetic techniques. Our findings present the first cytogenetic data for Trypoxylon rogenhoferi (2n = 30) and Trypoxylon albonigrum (2n = 32), while the karyotypes of Trypoxylon nitidum (2n = 30) and Trypoxylon lactitarse (2n = 30) were similar to those previously described. Fluorochrome staining and microsatellite distribution data revealed differences in the constitutive heterochromatin composition among species. Trypoxylon nitidum and T. albonigrum exhibited one major rDNA cluster, potentially representing an ancestral pattern for aculeate Hymenoptera, while T. rogenhoferi and T. lactitarse showed two pericentromeric rRNA gene sites, suggesting amplification events in their ancestral clade. The (TCAGG)n motif hybridized in the terminal regions of the chromosomes in all four Trypoxylon species, which may suggest that this sequence represents DNA telomeric repeat. Notably, the presence of this repetitive sequence in the centromeric regions of certain chromosome pairs in two species supports the hypothesis of chromosomal fusions or inversions in the ancestral karyotype of Trypoxylon. The study expands the chromosomal mapping data of repetitive sequences in wasps and offers insights into the dynamic evolutionary landscape of karyotypes in these insects.

Phylogenetic analysis of viviparity, matrotrophy, and other reproductive patterns in chondrichthyan fishes.

The reproductive diversity of extant cartilaginous fishes (class Chondrichthyes) is extraordinarily broad, reflecting more than 400 million years of evolutionary history. Among their many notable reproductive specialisations are viviparity (live-bearing reproduction) and matrotrophy (maternal provision of nutrients during gestation). However, attempts to understand the evolution of these traits have yielded highly discrepant conclusions. Here, we compile and analyse the current knowledge on the evolution of reproductive diversity in Chondrichthyes with particular foci on the frequency, phylogenetic distribution, and directionality of evolutionary changes in their modes of reproduction. To characterise the evolutionary transformations, we amassed the largest empirical data set of reproductive parameters to date covering nearly 800 extant species and analysed it via a comprehensive molecular-based phylogeny. Our phylogenetic reconstructions indicated that the ancestral pattern for Chondrichthyes is 'short single oviparity' (as found in extant holocephalans) in which females lay successive clutches (broods) of one or two eggs. Viviparity has originated at least 12 times, with 10 origins among sharks, one in batoids, and (based on published evidence) another potential origin in a fossil holocephalan. Substantial matrotrophy has evolved at least six times, including one origin of placentotrophy, three separate origins of oophagy (egg ingestion), and two origins of histotrophy (uptake of uterine secretions). In two clades, placentation was replaced by histotrophy. Unlike past reconstructions, our analysis reveals no evidence that viviparity has ever reverted to oviparity in this group. Both viviparity and matrotrophy have arisen by a variety of evolutionary sequences. In addition, the ancestral pattern of oviparity has given rise to three distinct egg-laying patterns that increased clutch (brood) size and/or involved deposition of eggs at advanced stages of development. Geologically, the ancestral oviparous pattern arose in the Paleozoic. Most origins of viviparity and matrotrophy date to the Mesozoic, while a few that are represented at low taxonomic levels are of Cenozoic origin. Coupled with other recent work, this review points the way towards an emerging consensus on reproductive evolution in chondrichthyans while offering a basis for future functional and evolutionary analyses. This review also contributes to conservation efforts by highlighting taxa whose reproductive specialisations reflect distinctive evolutionary trajectories and that deserve special protection and further investigation.

Evolution of ancient satellite DNAs in extant alligators and caimans (Crocodylia, Reptilia)

BackgroundCrocodilians are one of the oldest extant vertebrate lineages, exhibiting a combination of evolutionary success and morphological resilience that has persisted throughout the history of life on Earth. This ability to endure over such a long geological time span is of great evolutionary importance. Here, we have utilized the combination of genomic and chromosomal data to identify and compare the full catalogs of satellite DNA families (satDNAs, i.e., the satellitomes) of 5 out of the 8 extant Alligatoridae species. As crocodilian genomes reveal ancestral patterns of evolution, by employing this multispecies data collection, we can investigate and assess how satDNA families evolve over time.ResultsAlligators and caimans displayed a small number of satDNA families, ranging from 3 to 13 satDNAs in A. sinensis and C. latirostris, respectively. Together with little variation both within and between species it highlighted long-term conservation of satDNA elements throughout evolution. Furthermore, we traced the origin of the ancestral forms of all satDNAs belonging to the common ancestor of Caimaninae and Alligatorinae. Fluorescence in situ experiments showed distinct hybridization patterns for identical orthologous satDNAs, indicating their dynamic genomic placement.ConclusionsAlligators and caimans possess one of the smallest satDNA libraries ever reported, comprising only four sets of satDNAs that are shared by all species. Besides, our findings indicated limited intraspecific variation in satellite DNA, suggesting that the majority of new satellite sequences likely evolved from pre-existing ones.

Transposable Element Insertions Are Associated with Batesian Mimicry in the Pantropical Butterfly Hypolimnas misippus.

Hypolimnas misippus is a Batesian mimic of the toxic African Queen butterfly (Danaus chrysippus). Female H. misippus butterflies use two major wing patterning loci (M and A) to imitate three color morphs of D. chrysippus found in different regions of Africa. In this study, we examine the evolution of the M locus and identify it as an example of adaptive atavism. This phenomenon involves a morphological reversion to an ancestral character that results in an adaptive phenotype. We show that H. misippus has re-evolved an ancestral wing pattern present in other Hypolimnas species, repurposing it for Batesian mimicry of a D. chrysippus morph. Using haplotagging, a linked-read sequencing technology, and our new analytical tool, Wrath, we discover two large transposable element insertions located at the M locus and establish that these insertions are present in the dominant allele responsible for producing mimetic phenotype. By conducting a comparative analysis involving additional Hypolimnas species, we demonstrate that the dominant allele is derived. This suggests that, in the derived allele, the transposable elements disrupt a cis-regulatory element, leading to the reversion to an ancestral phenotype that is then utilized for Batesian mimicry of a distinct model, a different morph of D. chrysippus. Our findings present a compelling instance of convergent evolution and adaptive atavism, in which the same pattern element has independently evolved multiple times in Hypolimnas butterflies, repeatedly playing a role in Batesian mimicry of diverse model species.

Phylogenetic analyses of the subfamily Scarabaeinae (Coleoptera: Scarabaeidae) provide new insights into the Mexican Transition Zone theory.

Being areas of biotic overlap located between biogeographic regions, transition zones function as natural laboratories. The present study explores the phylogenetic history of the dung beetle subfamily Scarabaeinae, in order to present an evolutionary scenario that allows inference of the biogeographic history of the Mexican Transition Zone (MTZ) and integration of the distributional patterns of its biota. The species sampling included 94 New World taxa (93 species of Scarabaeinae and one species of Aphodiinae). The phylogenetic relationships of the main clades recovered in our study were supported with PP values 0.95. Based on the BAYAREALIKE model to reconstruct the ancestral distributional patterns of Scarabaeinae, we inferred a complex scenario with 19 dispersal events, 15 vicariance events, and three extinctions. We suggest that the Ancient Neotropical and Tropical Paleoamerican patterns represent the most likely ancestral distributional patterns for the Scarabaeinae of the MTZ, which probably settle there during the Eocene-Oligocene. The rest of the Scarabaeinae distributional patterns were assembled in subsequent periods. The results suggest that the MTZ had two separate formation stages: a Paleo-MTZ (Eocene-Miocene) and a current MTZ (Pliocene-Anthropocene). We conclude that the evolutionary history as well as the dispersal-vicariance scenario for the Scarabaeinae of the MTZ fits the out of the tropics model.

Taxonomic Structure and Wing Pattern Evolution in the Parnassius mnemosyne Species Complex (Lepidoptera, Papilionidae).

In our study, using the analysis of DNA barcodes and morphology (wing color, male genitalia, and female sphragis shape), we show that the group of species close to P. mnemosyne comprises the western and eastern phylogenetic lineages. The eastern lineage includes P. stubbendorfii, P. glacialis, and P. hoenei. The western lineage includes three morphologically similar species: P. mnemosyne (Western Eurasia), P. turatii (southwestern Europe), and P. nubilosusstat. nov. (Turkmenistan and NE Iran), as well as the morphologically differentiated P. ariadne (Altai). The latter species differs from the rest of the group in the presence of red spots on the wings. Parnassius mnemosyne s.s. is represented by four differentiated mitochondrial clusters that show clear association with specific geographic regions. We propose to interpret them as subspecies: P. mnemosyne mnemosyne (Central and Eastern Europe, N Caucasus, N Turkey), P. mnemosyne adolphi (the Middle East), P. mnemosyne falsa (Tian Shan), and P. mnemosyne gigantea (Gissar-Alai in Central Asia). We demonstrate that in P. ariadne, the red spots on the wing evolved as a reversion to the ancestral wing pattern. This reversion is observed in Altai, where the distribution areas of the western lineage, represented by P. ariadne, and the eastern lineage, represented by P. stubbendorfii, overlap. These two species hybridize in Altai, and we hypothesize that the color change in P. ariadne is the result of reinforcement of prezygotic isolation in the contact zone. The lectotype of Parnassius mnemosyne var. nubilosus Christoph, 1873, is designated.

Abstract B060: Hereditary cancer testing across race and ethnicity: Differences in patient characteristics and genetic test results

Abstract Rates of pathogenic/likely pathogenic variants (PGVs) and variants of uncertain significance (VUS) in genes associated with hereditary cancer syndromes vary across race and ethnicity. Here, we report on differences in physician orders and test results across race and ethnicity in patients referred for hereditary cancer testing at a single laboratory in the United States. Patients (N=109,264) with self-reported Ashkenazi Jewish (AJ; N=2,788), Black (N=19,538), East Asian (E Asian; N=1,953), Hispanic (N=19,920), South East Asian (SE Asian; N=845), South Asian (S Asian, N=626), and White (N=63,594) ethnicities who had hereditary cancer testing between 2020 and 2022 were included. Patient characteristics were summarized and genetic test results were compared (Chi-Square test, White as the reference group). Across all races and ethnicities, most patients were female (94-96%) and reported a family history of cancer (88-96%), while 29%-32% reported a personal history of cancer. Mean age at testing varied across groups (AJ 48.4±15.5 years, Black 43.4±13.5 years, E Asian 45.1±12.8 years, Hispanic 42.8±13.2 years, SE Asian 45.2±13.2 years, S Asian 43.9±14.4 years, White 46.1±14.3 years). The number of genes tested (small panel <20, medium panel 20-53, large panel >53) varied across ethnicities: White (14%, 80%, 5.4%), AJ (8.2%, 86%, 5.6%), Black (14%, 83%, 3.1%), E Asian (9.2%, 88%, 2.4%), Hispanic (15%, 81%, 4.5%), S Asian (15%, 82%, 3.2%), SE Asian (12%, 82%, 5%). Compared to White patients (10%), PGV rates were significantly lower in Black (4.7%, p<0.0001), E Asian (5.2%, p<0.0001), Hispanic (6.5%, p<0.0001), and SE Asian (4.3%, p<0.0001) patients, and significantly higher in AJ patients (15%, p<0.0001). No differences were observed compared with S Asian patients (7.7%, p=0.0522). Across all groups, most patients with PGVs had findings in actionable genes (AJ 96%, Black, 81%, E Asian 92%, Hispanic 88%, S Asian 90%, SE Asian 94%, White 86%). The most common genes with actionable PGVs were BRCA2 (Black, E Asian, SE Asian), CHEK2 (AJ, White), and MUTYH (Hispanic, S Asian). VUS rates, in the absence of any PGVs, when compared with White patients (20%) were significantly higher in Black (29%, p<0.0001), E Asian (34%, p<0.0001), Hispanic (25%, p<0.0001), S Asian (33%, p<0.0001), and SE Asian (38%, p<0.0001) patients, and were significantly lower in AJ patients (12%, p<0.0001). For all races and ethnicities, the two most common genes with VUS were ATM and APC. In this relatively diverse sample (~36% Hispanic or Black), these data demonstrate that there are variations in hereditary cancer testing with respect to provider ordering patterns (i.e., patient age, panel size) and test results (i.e., PGV rates) across ethnicities. These differences may reflect ancestral PGV patterns, other biologic correlates, or variable application of selection criteria. As previously reported, VUS rates are higher in non-White patients. Improved access to testing and additional evidence generation across all races and ethnicities will help to improve variant curation. Citation Format: Shifra Krinshpun, Breeana L. Mitchell, Jingwen Zhang, Nicholas Sun, Sara L. Bristow, Antony Tin, Minetta C. Liu, Adam ElNaggar, Alexey Aleshin, Jeffrey N. Weitzel. Hereditary cancer testing across race and ethnicity: Differences in patient characteristics and genetic test results [abstract]. In: Proceedings of the 16th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2023 Sep 29-Oct 2;Orlando, FL. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2023;32(12 Suppl):Abstract nr B060.

Mitochondrial phylogenomics of the Australian scribbly gum moth Ogmograptis (Lepidoptera: Bucculatricidae) and an examination of deep‐level relationships within Lepidoptera

AbstractLarval feeding by the moth genus Ogmograptis (Bucculatricidae: Lepidoptera) creates one of the most iconic features of the Australian bush—the ‘scribbles’ found on smooth‐barked Eucalyptus. The taxonomic history of Ogmograptis has been challenging, with members of the genus being initially described in four different genera representing three different superfamilies. While prior phylogenetic analysis has placed Ogmograptis within the Bucculatricidae, these findings were not strongly supported and there was poor resolution of the early diverging, non‐Apoditrysia superfamilies that Ogmograptis has been assigned to by different authors. As a consequence, the unique larval biology of scribbly moths cannot yet be interpreted in an evolutionary context. Phylogenomic analysis of whole mitochondrial (mt) genome data for Ogmograptis, related non‐Apoditrysia and taxa representing the superfamily‐level diversity of the order strongly supports its placement within the Bucculatricidae, a monophyletic Gracillarioidea and a clade of Gracillarioidea + Yponomeutoidea that was sister to the Apoditrysia. The hypermetamorphic larval development in Ogmograptis can thus be interpreted as an elaboration of the ancestral pattern of the clade Gracillarioidea + Yponomeutoidea that has specialised for phellogen/callus feeding within the bark. The utility of mt genomes for deep‐level phylogenetic study of the Lepidoptera is reviewed against prior multi‐locus and nuclear phylogenomic datasets. Mt phylogenomic analyses are sensitive to analytical methods and the inclusion versus exclusion of high‐variability data partitions for deep‐level relationships, already shown to be uncertain by multi‐locus or nuclear phylogenomic analyses, in particular relationships between apoditrysian and obtectomeran superfamilies. While mt genomes are ideal for examining the relationships of rare, physically small or difficult to collect taxa such as Ogmograptis, due to the low technical hurdles to collecting whole genomes, continued attention to the analytical sensitivities of phylogenies that use this data source is needed to reliably advance our understanding of deep lepidopteran evolution.

Reconstructing the origin and early evolution of the snake brain.

Snakes represent one-eighth of terrestrial vertebrate diversity, encompassing various lifestyles, ecologies, and morphologies. However, the ecological origins and early evolution of snakes are controversial topics in biology. To address the paucity of well-preserved fossils and the caveats of osteological traits for reconstructing snake evolution, we applied a different ecomorphological hypothesis based on high-definition brain reconstructions of extant Squamata. Our predictive models revealed a burrowing lifestyle with opportunistic behavior at the origin of crown snakes, reflecting a complex ancestral mosaic brain pattern. These findings emphasize the importance of quantitatively tracking the phenotypic diversification of soft tissues-including the accurate definition of intact brain morphological traits such as the cerebellum-in understanding snake evolution and vertebrate paleobiology. Furthermore, our study highlights the power of combining extant and extinct species, soft tissue reconstructions, and osteological traits in tracing the deep evolution of not only snakes but also other groups where fossil data are scarce.

The First Genome-Wide Mildew Locus O Genes Characterization in the Lamiaceae Plant Family.

Powdery mildew (PM) is a widespread plant disease that causes significant economic losses in thousands crops of temperate climates, including Lamiaceae species. Multiple scientific studies describe a peculiar form of PM-resistance associated at the inactivation of specific members of the Mildew Locus O (MLO) gene family, referred to as mlo-resistance. The characterization of Lamiaceae MLO genes, at the genomic level, would be a first step toward their potential use in breeding programs. We carried out a genome-wide characterization of the MLO gene family in 11 Lamiaceae species, providing a manual curated catalog of 324 MLO proteins. Evolutionary history and phylogenetic relationships were studied through maximum likelihood analysis and motif patter reconstruction. Our approach highlighted seven different clades diversified starting from an ancestral MLO domain pattern organized in 18 highly conserved motifs. In addition, 74 Lamiaceae putative PM susceptibility genes, clustering in clade V, were identified. Finally, we performed a codon-based evolutionary analysis, revealing a general high level of purifying selection in the eleven Lamiaceae MLO gene families, and the occurrence of few regions under diversifying selection in candidate susceptibility factors. The results of this work may help to address further biological questions concerning MLOs involved in PM susceptibility. In follow-up studies, it could be investigated whether the silencing or loss-of-function mutations in one or more of these candidate genes may lead to PM resistance.

New evidence of consistency between phylogeny and morphology for two taxa in ciliated protists, the subclasses Oligotrichia and Choreotrichia (Protista, Ciliophora)

Marine planktonic ciliates are largely oligotrichs and choreotrichs, which are two subclasses of the class Spirotrichea. The current phylogenetic assignments of oligotrichs and choreotrichs are inconsistent with previous results based on morphological features, probably hindered by the limited information from a single gene locus. Here we provide 53 new sequences from small subunit ribosomal RNA (SSU rDNA), ITS1-5.8S rDNA-ITS2, and large subunit ribosomal RNA (LSU rDNA) gene loci in 25 oligotrich and choreotrich species. We also predict RNA secondary structures for the ITS2 regions in 55 species, 48 species of which are reported for the first time. Based on these novel data, we make a more comprehensive phylogenetic reconstruction, revealing consistency between morphological taxonomy and an updated phylogenetic system for oligotrichs and choreotrichs. With the addition of data from ciliature patterns and genes, the phylogenetic analysis of the subclass Oligotrichia suggests three evolutionary trajectories, among which: 1) Novistrombidium asserts an ancestral ciliary pattern in Oligotrichia; 2) the subgenera division of Novistrombidium and Parallelostrombidium are fully supported; 3) the three families (Tontoniidae, Pelagostrombidiidae and Cyrtostrombidiidae) all evolved from the most diverse family Strombidiidae, which explains why strombidiids consistently form polyphyletic clades. In the subclass Choreotrichia, Strombidinopsis likely possesses an ancestral position to other choreotrichs, and both phylogenetic analysis and RNA secondary structure prediction support the hypothesis that tintinnids may have evolved from Strombidinopsis. The results presented here offer an updated hypothesis for the evolutionary history of oligotrichs and choreotrichs based on new evidence obtained by expanding sampling of molecular information across multiple gene loci.

Tempo‐spatial evolution of seed plant endemism in Taiwan island

AbstractAimIn Taiwan island, recent land‐bridge and oversea dispersal after the appearance of proto‐Taiwan (<6.5 Ma) is responsible for its biodiversity assembly. Radiations have also been widely reported in mountain systems. The tempo‐spatial route to the floral hotspot was determined through a meta‐analysis of the evolution of endemic plants.LocationTaiwan island and its adjacent regions.TaxonSeed plants.MethodsPublished dated phylogenies were compiled to infer the origin times represented by the stem ages. To determine the speciation mode, either in situ origin or dispersal origin, the ancestral range shift pattern and/or current distribution range of the sister taxa were used with 10 different biogeographical regions classified. Histograms quantifying the numbers of different origin modes within bins of 0.5 Ma were constructed. Probabilities of long‐distance dispersal (LDD) were evaluated.ResultsThe 125 sampled species originate between the late Eocene and late Pleistocene, of which 14 (11.2%) and 111 (88.8%) were derived before and after the emergence of proto‐Taiwan, respectively. Spatially, in situ speciation would have a bigger contribution to the formation of endemism than dispersal events (56.8% vs. 43.2%). The species with in situ origin (mean = 1.83 Ma) were significantly younger than those with dispersal origin (mean = 6.34 Ma). The main regions where dispersal occurred were South‐Central China (n = 29) and Southeast China (n = 28), followed by Japan (n = 14). High probabilities (60.8%) of LDD were found.Main ConclusionsSpatially, recent land‐bridge and oversea dispersal from the adjacent Asian flora is supported and the southern part of China was found to be the most important source. In situ speciation that may have correlated with mountain uplift, monsoon intensification and Pleistocene climatic fluctuations exerted greater contributions to the biodiversity there. Temporally, floral endemism predominantly occurred after the emergence of proto‐Taiwan. Additional investigations with more sophisticated sampling and genetic data are needed in the future.