Mark Nikolic

All Publications

• Building phenotypic character matrices for phylogenetic inference: exploration of 35 years of practice. Biological reviews of the Cambridge Philosophical Society Hopkins, M. J., Nikolic, M. C., Holmes, J. D., Monti, D. S., Vargas-Parra, E. E., Bicknell, R. D., Edgecombe, G. D., Jordan-Burmeister, K., Paterson, J. R., Srivastava-Losey, S. 2026

  Abstract

  Recent methodological development in phylogenetic inference has focused predominantly on molecular data. However, renewed interest in other data types, particularly morphological data, has followed from the increased recognition of the power of total evidence and tip-dating approaches, including fossil data, for inference of time-scaled trees and rates of evolution. However, attention has largely focused on the improvement of models of morphological evolution and other analytical tools with much less discussion about data acquisition itself. Here we review past and current practice for describing and collecting morphological data for phylogenetic inference. We present a systematic review of 164 phylogenetic analyses conducted over the last 35 years and focused on a diverse group of extinct arthropods: trilobites. Trends in increasing matrix size, data type, and coding strategy are evident. Where present, polymorphic characters have been predominantly derived from discretized continuous characters, although increasingly practitioners are utilizing alternative approaches for the treatment of quantitative characters. Not surprisingly, traditional indices that describe character consistency are highly correlated with matrix size but show surprising variation at different taxonomic scales. More recent attempts to describe data quality using information theory imply that characters can have high information content even if data are missing for many tips, providing support against the exclusion of characters because of missing data. In consideration of this, as well as advances in the study of developmental biology and variational complexity, we identify several avenues for increasing the quality and quantity of morphological data going forward.

  View details for DOI 10.1002/brv.70183

  View details for PubMedID 42157438

• Polynoidae (Annelida) from bathyal and abyssal depths in southern and eastern Australia RECORDS OF THE AUSTRALIAN MUSEUM Murray, A., Burghardt, I., Gunton, L. M., Nizar, N., Nikolic, M. C., Wilson, R. S. 2025; 77 (4): 193-269

  View details for DOI 10.3853/j.2201-4349.77.2025.1904

  View details for Web of Science ID 001587087500001

• Combining fossil taxa with and without morphological data improves dated phylogenetic analyses. Biology letters Nikolic, M. C., Warnock, R. C., Hopkins, M. J. 2025; 21 (8): 20250205

  Abstract

  The fossilized birth-death (FBD) model has become an increasingly popular method for inferring dated phylogenies. It is especially useful for incorporating fossil data into such analyses, integrating fossils along with their age information directly into the tree as tips or sampled ancestors. Two approaches are common for placing fossil taxa in trees: inference based on morphological character data or using taxonomic constraints to control their topological placement. These approaches have historically been treated as alternatives, and for phylogenetic inference of entirely extinct organisms, additional related fossil taxa other than those for which morphology is available are generally overlooked. Here, for the first time, we implement a combined approach on an empirical dataset for a group of trilobites. We use a morphological matrix and ages for 56 taxa and age information for another 196 taxa from the Paleobiology Database. To evaluate the effects of a combined approach, we conducted FBD-dated phylogenetic analyses using the combined dataset with morphology and taxonomic constraints and compared them to analyses of taxa with morphology alone. We find that a combined approach yields topologies that are more stratigraphically congruent, substantially more precise parameter estimates (e.g. divergence times) and more informative tree distributions. These findings are a consequence of the substantial increase in stratigraphic age information and a more representative sample of the temporal distributions of the group.

  View details for DOI 10.1098/rsbl.2025.0205

  View details for PubMedID 40795980

  View details for PubMedCentralID PMC12343125

• From fossils to phylogenies: exploring the integration of paleontological data into Bayesian phylogenetic inference PALEOBIOLOGY Mulvey, L. P. A., Nikolic, M. C., Allen, B. J., Heath, T. A., Warnock, R. C. M. 2025; 51 (1): 214-236

  View details for DOI 10.1017/pab.2024.47

  View details for Web of Science ID 001472368100009

• Shared patterns of segment size development in trilobites and vertebrates EVOLUTION Nikolic, M. C., Hopkins, M. J., Evans, A. R. 2023; 77 (6): 1479-1487

  Abstract

  The relative sizes of body segments are a major determinant of the shape and functionality of an animal. Developmental biases affecting this trait can therefore have major evolutionary implications. In vertebrates, a molecular activator/inhibitor mechanism, known as the inhibitory cascade (IC), produces a simple and predictable pattern of linear relative size along successive segments. The IC model is considered the default mode of vertebrate segment development and has produced long-term biases in the evolution of serially homologous structures such as teeth, vertebrae, limbs, and digits. Here we investigate whether the IC model or an IC-like model also has controls on segment size development in an ancient and hyperdiverse group of extinct arthropods, the trilobites. We examined segment size patterning in 128 trilobite species, and during ontogenetic growth in three trilobite species. Linear relative segment size patterning is prominent throughout the trunk of trilobites in the adult form, and there is strict regulation of this patterning in newly developing segments in the pygidium. Extending the analysis to select stem and modern arthropods suggests that the IC is a common default mode of segment development capable of producing long-term biases in morphological evolution across arthropods as it does in vertebrates.

  View details for DOI 10.1093/evolut/qpad057

  View details for Web of Science ID 000980149400001

  View details for PubMedID 37074198