The phrase “genome” is roughly 81 years old and describes either the entire collection of genes on chromosomes or the entire genetic makeup of an organism. It creates the phenotype of an individual along with the impact of an environment. The term “genomics” was first used by Thomas Roderick in 1986 to describe the scientific field that deals with the mapping, sequencing, and analysis of the genome. In the past, only model organisms could be used for genome analysis, but today, thousands of organisms, including plants, invertebrates, and vertebrates, have had their genomes sequenced, and the results have been annotated. Using new techniques in metabolomics, proteomics, and transcriptomics, the results have been further refined and augmented. Utilizing population genomic techniques, it is now much simpler to study the genetic variability, population structure, and recent demographic events of vulnerable species.
How did species change?
One of the most significant aspects of existence is without a doubt how species evolve. Evolution focuses on how two, three, or a full set of species might emerge from a single species, each one tailored to a different ecological niche. It also considers how a species adapts to survive environmental changes. We refer to this process as speciation. Speciation is one of the most controversial processes. Charles Darwin noted that he lacked an explanation for why living organisms are grouped into well-defined species as opposed to there being a continuous gradation between all organisms in his work titled, precisely, The Origin of Species. This chain would allow us to find organisms that are different from each other in a progressive way rather than the discontinuous way that we observe the different species.
Therefore, it becomes evident that some fundamental aspect of evolution favors the emergence of distinct species rather than a continuity of various organisms. It’s as if there were privileged locations in the “physical space of life,” points of stability where species collect, and points of instability where new species arise. Similarly to how matter in the universe is organized into stars and planets rather than being dispersed across space, living beings are concentrated in points of the space of life that reflect the species.
In any event, creating new species in the lab to research the process is difficult. But in the late 1980s, a team of scientists used an enclosure with three distinct habitats, including wet/dry, light/dark, and warm/cold, and allowed a starter population of laboratory flies to freely pick where to reside. After 35-generation subpopulations, fruitflies resulted in total reproductive isolation across subpopulations that used different spatiotemporal environments. E. Mayr an evolutionary biologist, defined species as groups of natural populations that interbreed and are reproductively isolated from other comparable groups. For flies, that is the emergence of novel species in terms of evolution.
Clearly, such trials with wild animals are unfeasible, and it is also difficult to observe how others originate from one ancestral species due to the long time required, so the topic of higher animal speciation must be approached using different ways. One of them is to investigate the genetic divergences of two distinct but closely related species and to investigate how these divergences can explain how both species separated.
Of glaciers and refugia
Climate changes have shaped the distribution of the world’s biota over the course of the Quaternary (In the geologic time scale, the Quaternary is the most recent and current of the three Cenozoic Era periods). Glacier ebbs and flows during this time drove inhabitants into numerous significant ice age refugia. Regardless of geography or size, these glacier refuges were the places where species survived the ice ages and contained some level of acceptable habitat. Populations within these refugia were constrained and frequently isolated, gradually differentiating genetically. When the ice sheets retreated, species colonized the new land in a leading-edge expansion, which led to a clinal decrease in genetic variation. However, when lineages from various refugia intermingled, there was an increase in genetic diversity in colonized populations. Refugia within refugia, or historical subdivision and population isolation, contributed to the preservation of genetic diversity. Additionally, some species survived in secret glacier refugia that had conditions that were almost favorable and could support at least some temperate flora and animals.
The locations and internal complexity of these major and enigmatic ice period refugia, as well as subsequent colonization of deglaciated terrain, appear to have affected the genetic structure and distribution of present biotas, such as in the Scrub Jaysel birds (genus: Aphelocoma).
A complicated taxonomy history
In terms of splitting, grouping, and re-splitting on expert ornithologists’ classification lists, the scrub-jays of North America have had a somewhat dynamic taxonomic history that has been hypothesized to be the result of hybridization between Mexican jays and western scrub-jays. Rapid divergence and repeated episodes of post-divergence gene flow during complex speciation can obscure phylogenetic relationships and species boundaries. Recent DNA investigations, however, provide a new window into the genealogical and evolutionary links of this distinctive group of birds. Complex speciation is frequent in North America, at least in part because of the continent’s cyclical Pleistocene glacial history, which implies continuous expansion or contractions of habitats and therefore continuous contacts or isolation of species habitats, and keeps in mind that, like in the case of flies, spatial or temporal isolation can result in the creation of new species.
Because their range throughout North America is structured by phylogeographic barriers with multiple cases of secondary contact between divergent lineages, the Aphelocoma genus is an excellent system for researching speciation and the likely significance of hybridization in the evolution of diversity. Moreover, this is a fairly diversified genus, allowing for population comparisons and tracing the evolution of features. Many groups in this genus have been widely investigated, particularly from a behavioral standpoint. Aphelocoma jays have a variety of social patterns, ranging from solitary breeding couples to sophisticated social networks that involve nest assistance, among others. For example, it has been said that planning for the future is a characteristic that only humans possess. Recent research, however, reveals that food caching in scrub-jays contradicts this idea. Western scrub-jays (Aphelocoma californica) are attentive to the condition of their caches at recovery and can make plans for tomorrow’s meal. They can relate their previous experience as thieves to the risk of future cache theft by another bird. Although these findings imply that scrub-jays are capable of planning for the future, it is debatable for new species to what extent these birds act independently of their current levels of desire.
A rigorous genomic reconstruction of evolutionary history conducted by researchers at the University of Kansas is capable of clarifying evolutionary history despite complex speciation and has revealed that two groups of scrub jays, one in Mexico and one in Texas, deserve to be recognized as distinct species. The study, published in Systematic Biology, also uses species tree reconstruction, demographic model testing, and tests for gene flow from genomic data to sketch a natural history of scrub jays, demonstrating how geographic changes over millennia separated and reunited groups of the birds, influencing gene flow between them. The team discovers fresh statistically supported evidence for the distinctness of a lineage indigenous to southern Mexico (Aphelocoma woodhouseii sumichrasti), and they also discover new genetic evidence for the species status of Aphelocoma woodhouseii texana, a Texas endemic lineage culminating in support for the lineage’s species status under any commonly used species definition. Finally, the researchers discovered that despite abundant evidence supporting the overall isolation and species status of the non sister California Scrub-Jay (Aphelocoma californica) and Woodhouse’s Scrub-Jay (Aphelocoma woodhouseii), complex signatures of both ancient and modern gene flow between these two species result in discordant gene trees (the evolutionary history is not the same for different parts of the genome) and complicated reconstructions of evolutionary history (Fig. 1). The comprehensive framework present in the study for interrogating species limits and evolutionary history provides a necessary road map for separating the effects of gene flow and incomplete lineage sorting (refers to the fact that species have not had enough time to accumulate sufficiently unique variations in their DNA sequences since their separation) in order to better understand the systematics of other groups with similarly complex evolutionary histories.
Figure 1. In terms of splitting, lumping, and re-splitting on the bird checklist, North American scrub-jays have had a rather dynamic taxonomic history. Recent genetic investigations, however, have shown that California Scrub-Jay and Woodhouse’s Scrub-Jay are independent taxa, and support two distinct species for the Texas and southern Mexico complex. Credits: firstname.lastname@example.org from https://www.surfbirds.com/index.php
Species delimitation and conservation in the face of current mass extinction
Many scientists have cautioned that we are in the midst of a mass extinction caused by humans rather than a catastrophic natural occurrence. The planet is losing enormous ecosystems and the essentials they supply, such as freshwater, pollination, and pest and disease management, as a result of anthropogenic biodiversity loss. The loss of a species extends back in time because with it all of its evolutionary histories come to an end. It is like a permanently severed branch on the tree of life. However, the loss extends beyond the defunct species and affects a large number of other species that depend on the former since they have evolved in close proximity to it. Many of them disappear along with the species to which they were related, and some of them are forced to alter. The ongoing advancement of molecular technology, particularly genomics, is critical to biodiversity conservation.
Advanced genomics based on DNA information aids in the identification of new species that are difficult to differentiate using classic taxonomic approaches.
The primary cause of the current extinction is the human species’ rapid evolution, which prompts abrupt changes in both terrestrial and marine ecosystems. Many species go extinct because they do not have time to adjust to new circumstances due to the rapid pace of change. However, current genomics enables us to pinpoint the genetic regions relevant for adaptation. It may also help us better comprehend microevolution by improving our grasp of selection, mutation, mat assertiveness, and recombination. Genomics aids in the identification of genes required for fitness and, ultimately, in the development of current and fast monitoring systems for endangered biodiversity.
Conservation genetics is primarily concerned with determining the link between species or populations, studying cross-species variation, and describing the relationships between species and their harmful processes. In the future, as genomics advances, we hope to be able to properly anticipate the survival of local populations as well as their capacity to adapt to climatic change and other anthropogenic pressures. Due to a population increase, human activities such as climate change will both accelerate over time.
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- Burt, D. B. & Peterson, A. T. Biology of Cooperative-Breeding Scrub Jays (Aphelocoma Coerulescens) of Oaxaca, Mexico. The Auk 110, 207–214 (1993).
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- Raby, C. R., Alexis, D. M., Dickinson, A. & Clayton, N. S. Planning for the future by western scrub-jays. Nature 445, 919–921 (2007).
- DeRaad, D. A., McCormack, J. E., Chen, N., Peterson, A. T. & Moyle, R. G. Combining Species Delimitation, Species Trees, and Tests for Gene Flow Clarifies Complex Speciation in Scrub-Jays. Syst. Biol. syac034 (2022) doi:10.1093/sysbio/syac034.
- Nguyen, T. N. et al. Dynamics of reduced genetic diversity in increasingly fragmented populations of Florida scrub jays, Aphelocoma coerulescens. Evol. Appl. 15, 1018–1027 (2022).