Whole‐genome resequencing reveals the pleistocene temporal dynamics of Branchiostoma belcheri and Branchiostoma floridae populations

Abstract

Global climatic fluctuations governed the ancestral demographic histories of species and contributed to place the current population status into a more extensive ecological and evolutionary context. Genetic variations will leave unambiguous signatures in the patterns of intraspecific genetic variation in extant species since the genome of each individual is an imperfect mosaic of the ancestral genomes. Here, we report the genome sequences of 20 Branchiostoma individuals by whole‐genome resequencing strategy. We detected over 140 million genomic variations for each Branchiostoma individual. In particular, we applied the pairwise sequentially Markovian coalescent (PSMC) method to estimate the trajectories of changes in the effective population size ( N e ) of Branchiostoma population during the Pleistocene. We evaluated the threshold of sequencing depth for proper inference of demographic histories using PSMC was ≥25×. The PSMC results highlight the role of historical global climatic fluctuations in the long‐term population dynamics of Branchiostoma . The inferred ancestral N e of the Branchiostoma belcheri populations from Zhanjiang and Xiamen (China) seawaters was different in amplitude before the first (mutation rate = 3 × 10 −9 ) or third glaciation (mutation rate = 9 × 10 −9 ) of the Pleistocene, indicating that the two populations most probably started to evolve in isolation in their respective seas after the first or third glaciation of the Pleistocene. A pronounced population bottleneck coinciding with the last glacial maximum was observed in all Branchiostoma individuals, followed by a population expansion occurred during the late Pleistocene. Species that have experienced long‐term declines may be especially vulnerable to recent anthropogenic activities. Recently, the industrial pollution and the exploitation of sea sand have destroyed the harmonious living environment of amphioxus species. In the future, we need to protect the habitat of Branchiostoma and make full use of these detected genetic variations to facilitate the functional study of Branchiostoma for adaptation to local environments.

A chromosome‐level genome of the mud crab (Scylla paramamosain estampador) provides insights into the evolution of chemical and light perception in this crustacean

“…The change of effective population size was correlated with the historical geographic changes. The decline of effective population size occurred at the late Pleistocene, at when the sea level had dropped significantly (Bi et al, 2020), that might responsible for the bottleneck event of mud crab populations; while the increase occurs after the end of the late Pleistocene.…”

“…The central bold line represents the inferred population size, and the 100 thin curves surrounding the central line are PSMC estimates generated using 100 sequences randomly resampled from the original sequence. The Pleistocene (2.58 Ma to 11.7 kya, Bi et al, 2020) was marked in light yellow background…”

Deep whole-genome resequencing sheds light on the distribution and effect of amphioxus SNPs

“…Previous studies have revealed a contradictory phenomenon that extreme phenotypic similarity and high-level genetic diversity [ 2 , 3 ] [ 7 – 11 ] co-exist in amphioxus populations. Early publication claimed that the polymorphism rate of amphioxus might be as high as 5.37% [ 3 ], while they are commonly observed to share similar phenotypic characteristics [ 10 ], including body length, asymmetric body shape, number of oral cirri, etc.…”

“…These works offer more options for subsequent resequencing experiments as researchers have higher chance to access the reference genome best representing their samples. On the basis above, several attempts have been made to build amphioxus variant datasets [ 10 , 11 ], yet the low sequencing depth causing loss of polymorphisms [ 10 ] might make them difficult to provide reliable evidence.…”

The Genetic Diversity of Two Subpopulations of Shenxian Pigs as Revealed by Genome Resequencing

“…Based on the whole-genome resequencing technology, the genetic structure of the two sub-populations of Shenxian pigs was discussed, and the evolutionary mechanism between the two populations was revealed at the molecular level, and all genetic information in the whole genome was accurately obtained, and the two populations were discovered to the greatest extent. Genetic variation(Bi et al2020).…”