Geobiology and palaeogenomics

Abstract

Geobiology is centered on interactions of the biosphere with the atmosphere, hydrosphere, and lithosphere. In deep time geobiology has focused on critical intervals of change for Earth and its biota. Such geobiological studies include data from palaeobiology, geochemistry and sedimentary geology within an interdisciplinary framework. Palaeogenomics has a variety of research agendas, and one of them is to understand the genes involved in key changes in the evolutionary history of life and when those genes and their interactions first evolved. The combination of geobiology and palaeogenomic studies is a powerful approach which leads to a more fundamental understanding of how Earth and life have changed through time. For example, linking palaeogenomic studies of biomineralization genes in modern organisms and when they first evolved in the Cambrian with geobiological studies of the impact this had on the production of carbonate sedimentary facies such as encrinites and the development of the Neritan ocean provides a unique perspective on how genes

The effect of long-term atmospheric changes on the macroevolution of birds

“…Evolutionary transformations of ecologically-related features in animals, including body size, morphology, physiology, and locomotor modes, are closely tuned to the physical factors of the environments they inhabit (Rayner, 2003;Shubin, 2008;Clack, 2012). In consequence, past changes in environmental conditions-atmospheric concentrations of O2 and CO2, temperature, and others-can explain (and potentially drive) a number of macroevolutionary patterns, including adaptive radiations (Graham et al 1995;Thomas, 1997;Cornette et al, 2002, Falkowski et al, 2005, Saarinen et al 2014, mass extinctions (Huey and Ward, 2005;Long et al, 2015), trends in body size (Braddy et al, 2008;Choo et al, 2014), and major habitat transitions (e.g., water-to-land, land-to-air) that are intimately connected to key genetic, morphological, biomechanical, and physiological transformations (Dudley 2000;Chiappe, 2007;Shubin, 2008;Clack, 2012;Bottjer, 2017).…”

Paleogenomics of echinoids reveals an ancient origin for the double-negative specification of micromeres in sea urchins

“…Using a paleogenomic approach (12,13), it is possible to incorporate deep time into an analysis of when GRN novelties arose and to infer the regulatory interactions directing the development of extinct organisms, thereby bringing forth a unique understanding of the evolution of GRNs and the body plans that they encode. Paleogenomics allows for the dating of the appearance of apomorphic GRNs, their subcircuits, and particular network linkages using a combination of the fossil record, statistically derived divergence dates, and comparative analyses of robust experimental data from extant organisms.…”

Molecular Paleobiology of the Echinoderm Skeleton

“…Analyses of the structure, arrangement, and number of genes and families of genes involved in skeletogenesis (the molecular and developmental processes that build the skeleton) laid the groundwork for the current, meticulous, understanding of the genetic regulatory mechanisms which orchestrate development of the larval skeleton in sea urchins (Oliveri et al, 2008, Rafiq et al, 2012, Rafiq et al, 2014, Shashikant et al, 2018, Ettensohn, 2009, Sharma and Ettensohn, 2010, Livingston et al, 2006. In addition to providing insight into how the regulatory genome directs the development of the larval skeleton, the publication of the sea urchin genome also allowed for novel, and creative, insight into the evolution of the echinoderm skeleton in deep time (Bottjer et al, 2006). With their manuscript entitled "Paleogenomics of Echinoderms", which was published alongside the S. purpuratus genome in a special issue of Science, Bottjer et al (2006) made one of the first explicit attempts to link the evolution of genes to the initial appearance of a morphological feature, in this case the echinoderm skeleton, in the fossil record.…”

“…In addition to providing insight into how the regulatory genome directs the development of the larval skeleton, the publication of the sea urchin genome also allowed for novel, and creative, insight into the evolution of the echinoderm skeleton in deep time (Bottjer et al, 2006). With their manuscript entitled "Paleogenomics of Echinoderms", which was published alongside the S. purpuratus genome in a special issue of Science, Bottjer et al (2006) made one of the first explicit attempts to link the evolution of genes to the initial appearance of a morphological feature, in this case the echinoderm skeleton, in the fossil record.…”