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Biology subjects

Miller, C. V.

Publications and source records attributed to Miller, C. V..

3 recordsLinked to original sources

Trophic diversity and evolution in Enantiornithes: a synthesis including new insights from Bohaiornithidae

The "opposite birds" Enantiornithines were the dominant birds of the Mesozoic, but our understanding of their ecology is still tenuous. In particular, diets of enantiornithine species have remained speculative until recently. While this new work has been effective at determining diet within groups of enantiornithines, diet data thus far has been too sparse to comment on larger trends in the diversity and evolution of enantiornithine ecology. We introduce new data on the enantiornithine family Bohaiornithidae, famous for their large size and strong teeth and claws. In tandem with previously-published data on the earlier-diverging pengornithids and later-diverging longipterygids, we comment on the breadth of enantiornithine ecology and potential patterns in which it evolved. Body mass, jaw mechanical advantage, finite element analysis of the jaw, and traditional morphometrics of the claws and skull are compared between bohaiornithids and living birds. The sample size for living bird body mass is over ten times larger than previous studies on longipterygid and pengornithid diet, with implications in interpreting their results. We find bohaiornithids to be ecologically diverse: Bohaiornis and Parabohaiornis are similar to living plant-eating birds; Longusunguis resembles raptorial carnivores; Zhouornis is similar to both fruit-eating birds and generalist feeders; and Shenqiornis and Sulcavis plausibly ate fish, plants, or a mix of both. This ecological diversity is wider than any other enantiornithine family studied previously, which may be driven by strengthening of the jaw relative to other early birds. This strong jaw would allow bohaiornithids to eat harder foods than other birds at the time, but their jaws were weaker than most "strong-jawed" living birds. With these reconstructions of diet in Bohaiornithidae, there is quantitative support for enantiornithines inhabiting nearly every trophic level. By combining these reconstructions with past dietary predictions for Longipterygidae and Pengornithidae, we predict the ancestral enantiornithine bird to have been a generalist which ate a wide variety of foods. This would suggest that the ecological diversity of enantiornithine birds represents specialisation in taking foods their ancestors were already eating, rather than many dramatic changes in diet. However, more quantitative data from across the enantiornithine tree is needed to refine this prediction. By the Early Cretaceous, enantiornithine birds had diversified into a variety of ecological niches in a similar way to crown birds after the K-Pg extinction, adding to the body of evidence that traits unique to crown birds (e.g. a toothless beak or cranial kinesis) cannot completely explain their ecological success.

paleontology↗

Cas12a-Capture: a novel, low-cost, and scalable method for targeted sequencing

Targeted sequencing remains a valuable technique for clinical and research applications. However, many existing technologies suffer from pervasive GC sequence content bias, high input DNA requirements, and high cost for custom panels. We have developed Cas12a-Capture, a low-cost and highly scalable method for targeted sequencing. The method utilizes preprogramed guide RNAs to direct CRISPR-Cas12a cleavage of double stranded DNA in vitro and then takes advantage of the resulting four to five nucleotide overhangs for selective ligation with a custom sequencing adapter. Addition of a second sequencing adapter and enrichment for ligation products generates a targeted sequence library. We first performed a pilot experiment with 7,176 guides targeting 3.5 megabases of DNA. Using these data, we modeled the sequence determinants of Cas12a-Capture efficiency, then designed an optimized set of 11,438 guides targeting 3.0 megabases. The optimized guide set achieves an average 64-fold enrichment of targeted regions with minimal GC bias. Cas12a-Capture variant calls had strong concordance with Illumina Platinum Genome calls, especially for SNVs, which could be improved by applying basic variant quality heuristics. We believe Cas12a-Capture has a wide variety of potential clinical and research applications and is amendable for selective enrichment for any double stranded DNA template or genome.

genomics↗

Three-dimensionally preserved 'Stage IIIb' fossil down feather supports developmental modularity in feather evolution

We describe a unique three-dimensionally preserved fossil down feather from the Late Cretaceous of Myanmar. Its morphology is highly congruent with Stage IIIb of the widely accepted Prum and Brush model of feather evolution-development. This makes the new specimen the first evidence of this developmental stage in the fossil record. The Stage IIIb diagnosis is robustly supported by the absence of a central rachis and by its paired barbules emanating from radially positioned barbs that are attached to a short calamus. Prum and Brushs model hypothesises a bifurcation in the evolution-development pathway at Stage III. Stage IIIa involves rachis development and branching into barbs. Stage IIIb involves branching of the barbs from the calamus and then further branching of the barbules from the barbs. These two pathways then converge into Stage IIIa+b where feathers produce a rachis, barbs and barbules in nested order, finally leading to Stage IV. Evolution-development studies on the morphogenesis of feathers have unequivocally shown that such feather branching can be controlled by BMP, Noggin, Shh and several other proteins. Therefore, molecular crosstalk can convert a barb into a rachis and vice versa. The topology of this down feather, consistent with specific patterns of modular protein-protein signalling already observed, provides the first definitive evidence that such signalling was responsible for the evolution of a diverse inventory of feather morphologies in non-avialan dinosaurs and early birds since the middle Jurassic.

paleontology↗