“Recognizing relatives” based on some genes and phenotypes is not reliable

For a long time, the construction of species relationship trees using species morphological characteristics and molecular data has been a common practice in many researches. In fact, when using these two methods to infer the evolution of species, there are often contradictory situations, but the relevant research is very limited.

On April 20, Cell published a study conducted by a joint Team of Chinese and Foreign scientists. The study not only published the results of the radiation explosion process of marsupial mammal species, reconstructed the evolutionary relationship of marsupial species, but also explained the mechanism of the above contradictions.

The study showed that during the rapid differentiation of species, some random events may also lead to similar phenotypes in distant species.

The human genome is not always most similar to that of chimpanzees

“As early as about 160 years ago, Darwin proposed that all living things on the earth now evolved from a common ancestor, and the process of continuous bifurcation and evolution of the common ancestor to form a group of present species constitutes the ‘tree of life’.” Feng Shaohong, the first author of the paper and a researcher at Zhejiang University, said that reconstructing the correct species relationship tree is the basis for evolutionary biology research and cross-species comparative research, which is crucial for us to reason about the origin process of various biological phenomena.

ACCORDING TO THE ABOVE MODEL OF SPECIES EVOLUTION, DIFFERENCES IN THE DNA SEQUENCES BETWEEN SPECIES CAN REFLECT THE DIFFERENTIATION PROCESS OF SPECIES, I.E. The more similar the DNA sequence, the closer species are to the Tree of Life. At the same time, the phenotype of species is determined by DNA, and the evolutionary relationship of species that theoretically carry similar phenotypes is closer. According to this corollary, both morphological characteristics and DNA data can be used to construct species relationship trees.

“But in fact, constructing species relationship trees using DNA data and morphological characteristics often yields contradictory results, and there is still a lack of research to explain why this contradiction occurs.” Bai Ming, co-first author of the paper and a researcher at the Institute of Zoology of the Chinese Academy of Sciences, said.

“We tend to observe this conflict between molecular and morphological trees in taxa that have experienced rapid divergence of species.” Corresponding author Zhang Guojie, a professor at the Center for life evolution research at Zhejiang University, pointed out that incomplete genealogical shunting is one of the reasons that may lead to the above situation. Multiple species differentiate from a common ancestor in a very short period of time, causing polymorphisms of certain ancestral genes to be randomly shunted into differentiated species, resulting in multiple species randomly retaining the same genotype.

In the case of humans, chimpanzees, and gorillas, humans are more closely related to chimpanzees than gorillas. Most gene regions also show that humans and chimpanzees are closer, but in more than 15% of the human genome region, humans are more similar to gorillas and more different from chimpanzees. An A gene can be hypothesized to explain this phenomenon. The A gene in the population of the common ancestor of the three has a high genetic diversity, and the gorilla forms after the first species differentiation, and over time, the gorilla population eventually fixes a certain type (such as A1). The common ancestor group of humans and chimpanzees inherited two types (A1 and A2), however at the time of the second species differentiation, humans may end up randomly fixing A1 like gorillas, while chimpanzees eventually randomly fixed A2. As a result, we observe that some of the genome sequences of humans are more similar to gorillas and more different from chimpanzees.

This incomplete spectral shunt phenomenon has occurred in many taxa that have experienced large species explosions. A study by Zhang Guojie’s research group published in Science in 2014 revealed that this phenomenon is widespread in birds, which may be an important reason for the complexity of bird species relationship trees. In 2021, the research group revealed that this phenomenon is common in the process of fruit fly differentiation. However, whether this phenomenon has an impact on the evolution of species traits has been poorly studied.

Constructing species relationship trees based on partial genes and phenotypes is unreliable

To understand the effects of incomplete phylogenetic shunts on the evolution of species morphology and traits, the paper’s researchers used marsupials to conduct the study. This taxon is likely to have experienced a species explosion that has led to a long-standing controversy over its early evolutionary relationships, particularly in south American marsupial microphytes.

“The little mountain monkey is the only extant species of Marsupial micro-mammals in South America.” 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.” ”

Photo by Roberto F. Nespolo, a mountain monkey in a lair

It is precisely because of this similarity of phenotypes that the earlier evolutionary relationship based on the presumption of morphological characteristics suggests that the small mountain monkey and the bicient kangaroo and koala are closer, and then speculate that the American small mountain monkey originated in Australia.

However, the new study uses genome-wide data from the little mountain monkey and other marsupials to show that the little mountain monkey should be the sister group of all marsupials in Australia. That is, it shares a common ancestor with the Australian marsupials but does not belong to the Australian marsupials.

Further analysis revealed that the molecular tree constructed in more than 50% of the marsupial genome was inconsistent with the real species differentiation process, and the similarity between the small mountain monkey and some Australian marsupials was greater than the similarity between The Australian marsupials. The researchers speculate that earlier observations of phenotypic features that do not correspond to the occurrence of real species are likely due to incomplete lineage shunts during rapid differentiation of species.

To test the above conjecture, the researchers used specimens from the museum collection to determine that the humeral curvature morphology, spinal spinous height, and front tooth morphology of the small mountain monkey were more similar to those of kangaroos and koalas of the order Bicientes. Subsequently, the research team used comparative genomics analysis to screen candidate genes, and used gene editing technology to establish mouse experimental models for genes affected by incomplete lineage shunts. By comparing the results of skeletal phenotypic scans in mice and wild mice, the researchers confirmed that genotype replacements affected by incomplete lineage shunts did produce phenotypic results that matched expectations.

The evolution of species phenotypes is considered to be the result of the long-term adaptation of species to the environment, that is, mutations produce new genes and new phenotypes, and new genes spread through reproduction. Phenotypes and genes that favor survival and reproduction are preserved by natural selection. For cases where the same phenotype occurs in distant species, convergent evolution has tended to explain this phenomenon in the past. However, the study revealed that the appearance of the same phenotype between different taxa may also be caused by the random inheritance of ancestral phenotypes.

The researchers said that this study shows that it is unreliable to rely only on part genes and part phenotypes to build species relationship trees, and genome-wide data is the gold standard for reconstructing the evolution of species. Moreover, incomplete spectral shunts can be used as a mechanism to explain the conflict between genomic species relationship trees and phenotypic variations. (Source: China Science Daily Zhang Wenjing)

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