Abstract The explosion of different “omic” technologies and methods has led to many advances in ecology, evolution, and developmental biology, identifying countless novel phenotypes and molecular variants of interest as well as establishing new biological principals. The logical next step is to integrate these methods to deepen our understanding of these phenotypes and uncover biologically meaningful relationships, yet the pace of this advancement has been slow. Omic data is inherently high dimensional and identifying structure through the vast amounts of background noise remains a challenge across multiple connected fields and methodologies. Various sources of omic data and their associated methodologies can be integrated to understand the genomic underpinnings of phenotypic variation. The utilisation of high dimensional morphological and molecular phenotypes can be used to uncover the complex molecular and developmental bases of these traits. We present current, and potential future, methods for integrating multiple omic data types to identify biologically relevant phenotypic patterns. We also highlight that the integration of developmental theories into multi-omic analyses will help better understand the evolution of complex phenotypes. Here we provide a roadmap for navigating the integration of complex and high dimensional datasets using a wholistic and integrative approach between ecology, evolution, and development.

Biogeography is a discipline that aims to integrate multiple fields of inquiry to understand the spatial distribution of organisms. It draws from the fields of ecology, evolution, geography, geology, and Earth history to provide an explanation about what lives where and why. A specific subdiscipline of biogeography is vicariance biogeography, which focuses on the process of vicariance—the physical separation of a population, typically by a geographic barrier—as the source of new species. Vicariance biogeography thus attempts to explain the distribution of organisms that have achieved their place through a process of cladogenesis due to the emergence of a barrier, such as a newly formed body of water, a new mountain range, a newly established water current, etc. Such structures will prevent gene flow most readily in organisms that display low vagility or a narrow ecological tolerance. A paradigmatical example of vicariance biogeography is the signature that the breakup of Gondwana left on its biota, as such organisms achieved their modern distribution while riding on tectonic plates, which now allows us to trace the geological history of the continents’ movements. Traditionally approached by generating area cladograms—evolutionary trees that substituted taxa for geographic areas—today requires a temporal framework to justify the process of vicariance and distinguish it from dispersal. Vicariance is still found as the preferred biogeographical explanation for many groups of non-volant organisms that do not have a dispersal phase (e.g., certain kinds of larvae, seeds, or resistant bodies). However, many traditional examples of vicariance biogeography (e.g., the distribution of modern ratites or the Southern beech) are now rejected by evolutionary studies that have included a timed phylogeny. It is also well accepted that dispersal continues to play an important role in the distributions of many other organisms.

Amniota is the name assigned to a large group of limbed vertebrates that includes not only extant reptiles, birds, and mammals because of their reproductive strategy involving the amniotic egg, but also a rich record of extinct animals whose reproductive mode cannot be determined directly. The origin of amniotes is therefore anchored by two disparate disciplines: developmental biology and vertebrate paleontology. The amniotic egg is at the center of the great evolutionary success of the crown group Amniota. The developmental strategy of amniotes is characterized by the evolutionary innovation of a series of four extraembryonic membranes—the yolk sac, allantois, chorion, and amnion—that provide a complete developmental environment for the embryonic life of a reptile, bird, or mammal. These extraembryonic membranes allowed the common ancestor of amniotes and its descendants to invest the mother’s resources into fewer but larger eggs; protect the developing embryos by placing them in a nest or retain them in the reproductive canal; and therefore also eliminate the need for a prolonged larval stage and metamorphosis. It has been suggested that this evolutionary innovation provided an unprecedented opportunity to complete the conquest of the terrestrial realm by amniotes and has led to the great success of aquatic reptiles, Mesozoic dinosaurs and their descendants, the birds, and the Cenozoic mammals, including humans. Interestingly, it also appears to have been instrumental in allowing amniotes to invade other parts of the biosphere, including the air, through flying or gliding organisms, and even to return repeatedly to the aquatic environment. The fossil record of crown amniotes is very rich and extends over at least 318 million years of earth’s history, providing a detailed accounting of the evolutionary history of Amniota. As such, they provide the primary evidence for the origin and early evolution of this important clade of animals. Unfortunately, the fossil record is quite limited in the preservation of amniotic eggs, with the oldest documented evidence of fossilized amniotic eggs being those of 195-million-year-old dinosaurs. Thus, the origin and early diversification of amniotes, the transition from anamniotes to amniotes, and the composition of crown Amniota can only be determined by studies of the fossil record and through phylogenetic analyses. Since the fossil record of amniotes and their presumed close relatives is represented mainly by the remains of their bony skeletons, analyses can only be based on the morphological information provided by the skeletons of these ancient limbed vertebrates. The results of these analyses will determine the nature not only of the anamniote-amniote transition, but also the composition of crown Amniota, even in the absence of direct evidence of their embryology.

Several rodent genera radiated in Ethiopian highlands during Pleistocene, giving rise to species specialized to different elevation zones. The zonation is accompanied by vegetation change from savannahs or forests in lower elevations, through the mid-elevation belt of ericaceous shrublands to Afroalpine moorlands on the mountain tops. Such evolution on elevation gradient is expected to promote phenotypic adaptations and several genera are known to include highly distinctive high-elevation specialists. In this study, we systematically examined shape and size differentiation of skull and mandible in three genera, Lophuromys, Arvicanthis and Stenocephalemys, each including from six to eight species inhabiting different elevation zones on both sides of the Great Rift Valley. Employing computed tomography, three-dimensional virtual models, landmark-based geometric morphometrics and a powerful toolkit of partial least squares analysis, we demonstrated the elevation-related differentiation is a prominent feature of skull and mandible shape variation in all three genera. We identified the parts of skull and mandible which change most between the successive zones. These include, notably, orbits and insertion areas of masticatory muscles, which suggests adaptive shifts in visual perception and diet. We also showed that while the same parts are modified in all three genera, they are modified in different ways and to a different degree. The evidence for size differentiation was mixed despite the universal trend of larger size in higher elevations. Our study confirms the high-elevation specialists represent the most distinctive forms, which is especially true for the species from Bale and Arsi Mountains, East of the Great Rift Valley.

Body size of organisms is often associated with physiological demands and habitat structure. Several theories and models have been proposed to explain body size trends across geographical space and evolutionary time. It is proposed that herbivores are larger due to their more voluminous digestive system, allowing a longer retention time of the digested material. Simultaneously, for carnivores, it is expected that the bigger the prey, the larger the predator. Additionally, some body size trends have been attributed to climatic variation across space and habitat structure. Bergmann’s Rule proposes that larger endotherms inhabit colder areas, once a larger body size promotes better heat retention due to reduced surface/volume ratio. Similarly, aquatic endotherms are larger than expected, due to analogous physiological demands to endotherms living in colder environments. Here we tested whether body size of the Mustelidae clade can be explained by diet, habitat structure or environmental temperature. We performed phylogenetic regressions to assess the relationships between body size and the aforementioned predictors in 53 species of Mustelidae. We found that neither diet nor temperature were related to body size evolution. However, habitat was related to body size, with semi aquatic species being larger. Mechanisms involving thermal inertia, predation pressure, better quality resources close to water and bone density are hypotheses that suggest larger body sizes evolution in semi-aquatic vertebrates. We highlight the importance of considering widely accepted ecological traits for large groups, at lower taxonomic levels, in order to expand our understanding of the maintenance of these standards on different scales.