Alexis Rojas

University of Helsinki | HY · Department of Computer Science

The hypothesis of the Great Evolutionary Faunas is a foundational concept of macroevolutionary research postulating that three global mega-assemblages have dominated Phanerozoic oceans following abrupt biotic transitions. Empirical estimates of this large-scale pattern depend on several methodological decisions and are based on approaches unable to...

Since the last Ice Age (ca 115 000-11 700 years ago), the geographical ranges of most plants and animals have shifted, expanded or contracted. Understanding the timing, geographical patterns and drivers of past changes in insect communities is essential for evaluating the biodiversity implications of future climate changes, yet our knowledge of lon...

Site-selectivity analysis of drilling predation traces may provide useful behavioral information concerning a predator interacting with its prey. However, traditional approaches exclude some spatial information (i.e., oversimplified trace position) and are dependent on the scale of analysis (e.g., arbitrary grid system used to divide the prey skele...

Analyzing relational data consisting of multiple samples or layers involves critical challenges: How many networks are required to capture the variety of structures in the data? And what are the structures of these representative networks? We describe efficient nonparametric methods derived from the minimum description length principle to construct...

Large-scale biogeographic provinces of Cretaceous ammonoids, as currently defined in the literature, were delimited using qualitative assessments of taxonomic inventories. Using aggregated species occurrences in the Paleobiology Database, we generated a geographic network to quantify connectivity of Albian epicontinental basins and used the flow-ba...

The notions of change, such as birth, death, growth, evolution and longevity, extend across reality, including biological, cultural and societal phenomena. Patterns of change describe how success and composition of every entity, from species to societies, vary across time. Languages develop into new languages, music and fashion continuously evolve,...

Measurement theory, a branch of applied mathematics, offers guiding principles for extracting meaning from empirical observations and is applicable to any science involving measurements. Measurement theory is highly relevant in paleobiology because statistical approaches assuming ratio-scaled variables are commonly used on data belonging to nominal...

The early Mesozoic witnessed evolution of novel bivalve groups and innovation of diverse ecologic strategies. Although some newly evolved groups disappeared (e.g., Harpax), some persist until today (e.g., Cuspidariidae, Thyasiridae). Harpax (Norian-early Toarcian) is a globally widespread genus and a secondary soft substrate recliner, cemented to s...

Identifying and understanding the large-scale biodiversity patterns in time and space is vital for conservation and addressing fundamental ecological and evolutionary questions. Network-based methods have proven useful for simplifying and highlighting important structures in species distribution data. However, current network-based biogeography app...

Drilling predation is a common reason for mortality of benthic mollusks but did not become common until the late Mesozoic. The scarcity of drill holes in the early Mesozoic fossil record limits our understanding of the evolution of drilling behavior and its role on shaping early Mesozoic marine communities. Here, we use drilling traces on several b...

Preserving adaptive capacities of coastal ecosystems in the Anthropocene requires an understanding of their natural variability prior to modern times. We quantified responses of nearshore molluscs assemblages to past environmental changes using 101 samples (∼57300 specimens) retrieved from the subsurface Holocene succession and present-day seabed o...

Paleobiologists often employ network-based methods to analyze the inherently complex data retrieved from geohistorical records. Because they lack a common framework for designing, performing, evaluating, and communicating network-based studies, reproducibility and interdisciplinary research are hampered. The high-dimensional and spatiotemporally re...

Analyzing relational data collected over time requires a critical decision: Is one network representation sufficient? Or are more networks needed to capture changing structures? While the choice may be evident in some cases, for example when analyzing a physical system going through abrupt changes between two known states, other datasets can pose m...

The Permo‐Triassic vertebrate assemblage zones (AZs) of South Africa's Karoo Basin are a standard for local and global correlations. However, temporal, geographical and methodological limitations challenge the AZs reliability. We analyse a unique fossil dataset comprising 1408 occurrences of 115 species grouped into 19 stratigraphic bin intervals f...

To connect structure, dynamics and function in systems with multibody interactions, network scientists model random walks on hypergraphs and identify communities that confine the walks for a long time. The two flow-based community-detection methods Markov stability and the map equation identify such communities based on different principles and sea...

Despite its importance as the larger component of the modern and Cenozoic brachiopod faunas in the Caribbean region, the ecology and habitat preferences of the terebratulid Tichosina remain poorly understood. We compiled feld observations from multiple sites in the Caribbean of Colombia (i.e., San Bernado Bank, Bahia Honda-Guajira, Puerto Escondido...

Hypergraphs offer an explicit formalism to describe multibody interactions in complex systems. To connect dynamics and function in systems with these higher-order interactions, network scientists have generalised random-walk models to hypergraphs and studied the multibody effects on flow-based centrality measures. Mapping the large-scale structure...

To connect structure, dynamics and function in systems with multibody interactions, network scientists model random walks on hypergraphs and identify communities that confine the walks for a long time. The two flow-based community-detection methods Markov stability and the map equation identify such communities based on different principles and sea...

Climate regions form the basis of many ecological, evolutionary and conservation studies. However, our understanding of climate regions is limited to how they shape vegetation: They do not account for the distribution of animals. Here we develop a network-based framework to identify important climates worldwide based on regularities in realized nic...

Hypergraphs offer an explicit formalism to describe multibody interactions in complex systems. To connect dynamics and function in systems with these higher-order interactions, network scientists have generalised random-walk models to hypergraphs and studied the multibody effects on flow-based centrality measures. But mapping the large-scale struct...

Despite its importance as the larger component of the modern and Cenozoic brachiopod faunas in the Caribbean region, the ecology and habitat preferences of the terebratulid Tichosina remain poorly understood. We compiled field observations from multiple sites in the Caribbean of Colombia (i.e., San Bernado Bank, Bahia Honda-Guajira, Puerto Escondid...

Sepkoski's hypothesis of Three Great Evolutionary Faunas that dominated Phanerozoic oceans represents a foundational concept of macroevolutionary research. However, the hypothesis lacks spatial information and fails to recognize ecosystem changes in Mesozoic oceans. Using a multilayer network representation of fossil occurrences, we demonstrate tha...

Although classifications of the Earth's climates date back to the ancient Greeks, the climatic regions shaping the distribution of animals remain poorly resolved. Here we present a classification of global climates based on regularities in realised niches of 3657 amphibians, 7204 reptiles, 10684 birds and 4574 mammals. We found 16 main climatic reg...

To understand how a complex system is organized and functions, researchers often identify communities in the system's network of interactions. Because it is practically impossible to explore all solutions to guarantee the best one, many community-detection algorithms rely on multiple stochastic searches. But for a given combination of network and s...

To understand how a complex system is organized and functions, researchers often identify communities in the system's network of interactions. Because it is practically impossible to explore all solutions to guarantee the best one, many community-detection algorithms rely on multiple stochastic searches. But for a given combination of network and s...

The Mesozoic fossil record of brachiopods in northern South America is relatively scarce and their biogeographical history is not well understood. Cretaceous brachiopods in this region are restricted to carbonate platforms of Colombia. Here we examine the brachiopod fauna from the middle part of the Rosablanca Formation near the town of Zapatoca, E...

Research on drilling predation, one of the most studied biological interactions in the fossil record, has been concentrated on prey with calcareous skeletons (e.g. molluscs, echinoids, rhynchonelliform brachiopods). Based on a compilation of literature sources and surveys of paleontological collections of the Florida Museum of Natural History and t...

Colombian brachiopod faunas have not been studied extensively. Only three brachiopod species have been reported from the Colombian Caribbean Sea so far, namely Argyrotheca barrettiana (Davidson, 1866), Terebratulina latifrons Dall, 1920, and the cosmopolitan Platidia anomioides (Scacchi & Philippi, 1844). In this work, brachiopods collected from de...

We conducted a laboratory study to determine drillhole siteselectivity patterns in the predatory behavior of Notocochlis unifasciata (Lamarck, 1822), which is a common naticid gastropod on the eastern Pacific coast of Central America, preying on two infaunal venerid bivalves – the thin-shelled and weakly ornamented Leukoma grata (Say, 1831) and the...

Sequence stratigraphy provides the tools to predict the occurrences of marine taxa and test hypotheses on the diversity of faunal assemblages in response to relative sea-level change. We examined this relationship during the Stratigraphic Paleobiology field course sponsored by the Paleontological Society in July 2014. The Mississippian Lodgepole Fm...

The Tibasosa Formation crops out in central Colombia over the Eastern Cordillera to the NE of Bogotá. The Tibasosa Formation of Renzoni was separated into four intervals: the basal member with conglomerates and sandstones, the lower calcareous members with marlstones and limestones, the intermediate sandstone member and the upper calcareous member...

A new terebratulid species, Hadrosia gracilis, from the Lower Cretaceous Rosablanca Formation in Central Colombia is described. The new method of three-dimensional reconstructions of the internal morphology of this taxon results in the subjective synonymization of the Nerthebrochinae in favour of the Sellithyridinae. The geographical distribution o...

Decapod crustacean specimens recently collected from new and previously reported localities of USA, Mexico, and Colombia, as well as a review of species of uncertain affinity, add important information to complete the descriptions and paleobiological knowledge of some Cretaceous primitive crabs. The stratigraphic range for the genus Cenomanocarcinu...

Decapod crustacean specimens recently collected from new and previously reported localities of USA, Mexico, and Colombia, as well as a review of species of uncertain affinity, add important information to complete the descriptions and paleobiological knowledge of some Cretaceous primitive crabs. The stratigraphic range for the genus Cenomanocarcinu...

Nine taxa represent the crustacean component of the Turonian fauna from the Eagle Ford Group limestones and marls that crop out in several quarries, northwest of Múzquiz, Coahuila, Mexico. Three crustacean taxa are found in common with deposits of similar age and paleoenvironment of the San Rafael Formation of Colombia. Planktic foraminifera, ammon...

Nine taxa represent the crustacean component of the Turonian fauna from the Eagle Ford Group limestones and marls that crop out in several quarries, northwest of Múzquiz, Coahuila, Mexico. Three crustacean taxa are found in common with deposits of similar age and paleoenvironment of the San Rafael Formation of Colombia. Planktic foraminifera, ammon...

Nueve taxa representan el componente de crustáceos de la fauna del Turoniano en las calizas y margas del Grupo Eagle Ford que aflora en varias canteras al noroeste de Múzquiz, Coahuila, México. Tres taxa de crustáceos se encuentran en común con depósitos de similar edad y paleoambiente de la Formación San Rafael en Colombia. Foraminíferos planctóni...