Today (April 20), "Incomplete lineage sorting and phenotypic evolution in marsupials" was published online in cell, the top international academic journal. Through comparative genomics of their whole genome data, this paper reveals that some random events in the rapid differentiation process of species may lead to similar phenotypes of distant species, and explains the mechanism of frequent conflict in the construction of species trees using morphological and molecular data.
"It also means that species that look more alike and have similar DNA are not necessarily close relatives." Feng Shaohong, the first author of the paper and the Shenzhen Huada Life Science Research Institute, said in an interview with the Beijing News reporter that reconstructing the correct species relationship tree is the basis for evolutionary biology research and cross-species comparative research, which is crucial for reasoning the origin process of various biological phenomena.
"Less reliable" species relationship trees
As early as the 19th century, Darwin mentioned in his book On the Origin of Species that all species on Earth today originally evolved from the same primitive life, the common ancestor theory. The process of the continuous bifurcation and evolution of this common ancestor to form the present species group constitutes the tree of life, from simple single-celled organisms to complex life forms, each species can find its closest neighbor species and recent common ancestor.
In the case of humans, for example, about 7 million years ago, humans and chimpanzees diverged from their common ancestor, ancient apes. Paleontine and Old World monkeys had the same ancestors about 28 million years ago, the earliest primate species ancestors date back 80 million years, and mammals on Earth today share a common ancestor about 200 million years ago.
According to the early Darwin model of species evolution, the difference in DNA sequence between species can reflect the differentiation process of species, that is, the more similar the DNA sequence, the closer species are to the tree of life. At the same time, the phenotype is determined by DNA, and the closer the evolutionary relationship of species carrying the same phenotype is theoretically. According to this inference, both morphological and DNA data can be used to construct species trees.
"But in reality, DNA data and morphological traits often yield contradictory results when extrapolating the evolution of species, and there is still a lack of research to explain why such contradictions exist." Bai Ming, the co-first author of the paper and a researcher at the Institute of Zoology of the Chinese Academy of Sciences, said.
The contradiction between molecular and morphological trees often occurs in taxa that have experienced rapid divergence of species. Professor Zhang Guojie, the corresponding author of the paper and now the director of the Center for Life Evolution Research at Zhejiang University, believes that incomplete lineage sorting is a cause that can lead to the above situation. Multiple species differentiate from a common ancestor in a very short period of time, so that the polymorphisms of certain ancestral genes are randomly shunted into different species that are differentiated, so that multiple species randomly retain the same genotype.
Studies have shown that incomplete lineage shunts also exist in the evolutionary history of primate species. Humans are more closely related to chimpanzees than gorillas.
Schematic diagram of incomplete lineage shunts based on humans, chimpanzees, and gorillas (two dots in each group represent an individual and each dot represents a gene). Courtesy of respondents
Feng Shaohong told reporters that the group as the common ancestor of the three has a high genetic diversity, and the gorilla is formed after the first species differentiation, and over time, the gorilla population eventually fixed a blue genotype. The common ancestors of humans and chimpanzees inherited the orange and blue genotypes, but at the time of the second species differentiation, humans may end up randomly fixing the same blue genotype as gorillas, and chimpanzees eventually fixing orange genotypes.
"As a result, we will observe that some of the genome sequences of humans are more similar to those of gorillas and more different from those of chimpanzees, even though chimpanzees are the closest species to humans." More than 15% of the genome regions in the human genome are more similar to gorillas. Feng Shaohong said that this incomplete phylogenetic shunting phenomenon has appeared in many taxa that have experienced large outbreaks of species, such as various mammal taxa, birds, insects, fish, etc., but whether this phenomenon has an impact on the evolution of traits has not been studied.
The little mountain monkey does not belong to the Australian bag family
In the evolution of species, species radiation explosions often occur. For example, in a relatively short period of time, a large number of biological clusters appear. But this concept of "short time" is not just a moment, it may last for tens of millions of years. What makes Feng Shaohong curious is what kind of evolutionary events will occur in the species during this process? And what kind of traces will be left on the genome and on the phenotype?
Using phenotypic traits and genomic information to determine kinship can vary. Feng Shaohong introduced, for example, dolphins and bats have the ability of echo localization, but they are far away from the evolutionary tree and belong to convergent evolution. While "gene infiltration" shapes the morphological diversity of butterfly wings, it will also bring difficulties to correctly infer the evolution of species.
Taking marsupial mammals as an example, previous studies have shown that marsupial mammals may have experienced radiation explosions, which has led to a long-term controversy in the academic community about their early evolutionary relationships, especially around the evolutionary status of the South American order Microbiotheria. To this end, the research team conducted research using marsupials.
The process of continental drift and the distribution of contemporary marsupials involved in this study. Courtesy of respondents
"The little mountain monkey is the only extant species of the order." Feng Shaohong said, "As a marsupial in South America, it is more similar to The Marsupials in Australia in many aspects such as bones, reproductive organs and brain structure, especially kangaroos, koalas and other dipterodonts." ”
It is precisely because of this morphological similarity that the evolutionary relationship based on the presumption of morphological characteristics suggests that the small mountain monkey should be closer to the kangaroos and koalas of the order Bicienta, and then speculates that the American small mountain monkey should originate in Australia.
But the study suggests that the little mountain monkeys should be sisters of Australia's marsupials and are not part of the Australian marsupials. Past misconceptions are likely to be the result of incomplete lineage shunts during rapid divergence of species.
According to reports, these conflicting genomic regions contain hundreds of genes related to the nervous system, immune system, bone morphology, etc., which may be related to the contradictions between the characteristics of today's species traits and the course of species occurrence.
The study speculates that the random fixation of ancestral polymorphisms triggered by incomplete lineage shunts may accidentally lead to two more distantly related species inheriting the same ancestral genotype. Although it is common sense that different ancestral genotypes produce different morphological characteristics, in the above cases, it may lead to a more similar phenotype in distant species than in closely related species.
In order to verify the above conjecture, Researchers such as Feng Shaohong compared specimens from a number of museum collections and concluded that the humeral curvature morphology, spinal spinous height, and front tooth morphology of the small mountain monkey are more similar to those of kangaroos and koalas of the order Bicienta. Feng Shaohong mentioned, "In order to be able to compare skeletal forms more comprehensively, we collected dozens of different skeletal maps on six marsupial species. ”
Subsequently, the research team used comparative genomics analysis to screen candidate genes, and used gene editing technology to establish mouse experimental models of genes affected by incomplete lineage shunts. By comparing the scan results of skeletal traits in experimental and wild mice, the researchers confirmed the conjecture that genotype replacement affected by incomplete lineage shunts did produce phenotypic results that matched expectations.
Genome-wide data is the "gold standard"
The evolution of species traits is thought to be the result of long-term adaptation of species to the environment: mutations produce new genes and new traits, new genes spread through reproduction, and traits and genes that are conducive to survival and reproduction are preserved by natural selection.
The occurrence of the same trait in distant species has tended to be explained by convergent evolution in the past. However, the study revealed that the appearance of the same trait between different taxa may also be caused by the random inheritance of ancestral traits.
According to reports, this study also proves that it is unreliable to build a species relationship tree only by relying on the traceability of some genes and some traits, and the whole genome data is the "gold standard" for reconstructing the occurrence process of species. Through the comparative analysis of genome-wide data, incomplete lineage shunts can be used as a possible mechanism to explain the conflict between genomic species trees and phenotypic variations.
"What stands out in genome-wide data is 'full.'" Feng Shaohong told reporters that according to the different purposes of the study, the genome can be divided into gene regions and intergene regions, and can also have different characteristic elements. These different regions may be subjected to selection pressures and evolutionary events in the process of speciation, and the inferred evolutionary process of the species may also be different. In order to obtain the most reliable and comprehensive evolutionary process, complete genomic information needs to be integrated. In addition, this study also synthesizes evidence from paleoclimate geography, species differentiation, morphology, DNA and other aspects to support the evolution of marsupial species.
It is worth noting that in recent years, the development of sequencing technology has brought genomics research into a new era of perfect reference genomes. "In the early days, due to limited technology, we could only do one or two genes to do genomes. But with the development of technology, it is very easy to measure a whole genome, and it can quickly complete the genome of many species. Technology is constantly developing rapidly, and new technologies can expand the accuracy of data and give us better means to carry out research work. But we also can't ignore the importance of scientific problems, because scientific problems will further promote technological development. Feng Shaohong said.
Beijing News reporter Zhang Jianlin
Edited by Chen Jing, proofread by Wu Xingfa