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Evolutionary Genetics

Evolutionary Genetics is a comprehensive sequencing service designed to offer an insightful interpretation of the evolution within a large group of individuals, based on genetic variations, including SNPs, InDels, SVs, and CNVs. This service encompasses all essential analyses needed to elucidate the evolutionary shifts and genetic characteristics of populations, including assessments of population structure, genetic diversity, and phylogenetic relationships. Moreover, it delves into studies on gene flow, enabling estimations of effective population size and divergence time. Evolutionary genetics studies yield valuable insights into the origins and adaptations of species.

At BMKGene, we offer two avenues for conducting evolutionary genetics studies on large populations: employing whole-genome sequencing (WGS) or opting for a reduced representation genome sequencing method, the in-house-developed Specific-Locus Amplified Fragment (SLAF). While WGS suits smaller genomes, SLAF emerges as a cost-effective alternative for studying larger populations with longer genomes, effectively minimizing sequencing costs.

Service Details


Demo Results

Featured publications

Service Advantages

1Evolutionary genetics

Takagi et al., The plant journal, 2013

● Comprehensive bioinformatic analysis: enabling the estimation of genetic diversity, which reflects the evolutionary potential of species, and revealing reliable phylogenetic relation between species with minimized influence of convergent evolution and parallel evolution

● Optional customized analysis: such as the estimation of divergence time and speed based on variations at nucleotide and amino acids level.

● Extensive Expertise and publication records: BMKGene has accumulated massive experience in population and evolutionary genetics projects for over 12 years, covering hundreds of species, etc. and contributed to over 80 high-level projects published in Nature Communications, Molecular Plants, Plant Biotechnology Journal, etc.

● Highly skilled bioinformatics team and short analysis cycle: with great experience in advanced genomics analysis, BMKGene’s team delivers comprehensive analyses with a swift turnaround time.

● Post-Sales Support: Our commitment extends beyond project completion with a 3-month after-sale service period. During this time, we offer project follow-up, troubleshooting assistance, and Q&A sessions to address any queries related to the results.

Service Specifications and requirements

Type of sequencing

Recommended population scale

Sequencing strategy

Nucleotide requirements

Whole Genome Sequencing

>30 individuals, with >10 individuals from each subgroup



Concentration: ≥1 ng/ µL

Total amount≥ 30ng

Limited or no degradation or contamination

Specific-Locus Amplified Fragment (SLAF)

Tag depth:


Number of tags:

<400 Mb: WGS is recommended

<1Gb: 100K tags

1Gb<genome<2Gb: 200K tags

>2Gb: 300K tags

Max 500k tags

Concentration ≥ 5 ng/µL

Total amount ≥80 ng

Nanodrop OD260/280=1.6-2.5

Agarose gel: no or limited degradation or contamination


Sample Requirements and Delivery

Sample Requirements:









 Visceral tissue








 Muscle tissue

 Mammalian blood







 Poultry/Fish blood



  Fresh Leaf    






  Cultured cell    















Service Work Flow

Sample QC

Experiment design

sample delivery

Sample delivery

Library Preparation

Library construction



Data analysis

Data analysis

After sale Services

After-sale services

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  • SLAF流程图 -8.4改-01

    Service includes analysis of population structure (phylogenetic tree, PCA, population stratification chart), population diversity, and population selection (linkage disequilibrium, selective sweep-selection of advantageous sites). The service can also included customized analysis (e.g. divergence time, gene flow).

    *Demo results shown here are all from genomes published with BMKGENE

    1.Evolution analysis contains construction of phylogenetic tree, population structure and PCA based on genetic variations.

    Phylogenetic tree represents taxonomic and evolutionary relationships among species with common ancestor.
    PCA aims to visualize closeness between sub-populations.
    Population structure shows the presence of genetically distinct sub-population in terms of allele frequencies.

    3-1Phylogenetic-tree 3-2PCA 3-3Population-structure

    Chen, et. al., PNAS, 2020

    2.Selective sweep

    Selective sweep refers to a process by which an advantageous site is selected and frequencies of linked neutral sites are increased and those of unlinked sites are decreased, resulting in reduction of regional.

    Genome-wide detection on selective sweep regions is processed by calculating population genetic index(π,Fst, Tajima’s D) of all SNPs within a sliding window (100 Kb) at certain step (10 Kb).

    Nucleotide diversity(π)

    Tajima’s D

    Fixation index(Fst)


    Wu, et. al., Molecular Plant, 2018

    3.Gene Flow


    Wu, et. al., Molecular Plant, 2018

    4.Demographic history


    Zhang, et. al., Nature Ecology&Evolution, 2021

    5.Divergence time


    Zhang, et. al., Nature Ecology&Evolution, 2021

    Explore the advancements facilitated by BMKGene’s evolutionary genetics services through a curated collection of publications:

    Hassanyar, A. K. et al. (2023) ‘Discovery of SNP Molecular Markers and Candidate Genes Associated with Sacbrood Virus Resistance in Apis cerana cerana Larvae by Whole-Genome Resequencing’, International journal of molecular sciences, 24(7). doi: 10.3390/IJMS24076238.

    Chai, J. et al. (2022) ‘Discovery of a wild, genetically pure Chinese giant salamander creates new conservation opportunities’, Zoological Research, 2022, Vol. 43, Issue 3, Pages: 469-480, 43(3), pp. 469–480. doi: 10.24272/J.ISSN.2095-8137.2022.101.

    Han, M. et al. (2022) ‘Phylogeographical Pattern and Population Evolution History of Indigenous Elymus sibiricus L. on Qinghai-Tibetan Plateau’, Frontiers in Plant Science, 13, p. 882601. doi: 10.3389/FPLS.2022.882601/BIBTEX.

    Wang, J. et al. (2022) ‘Genomic insights into longan evolution from a chromosome-level genome assembly and population genomics of longan accessions’, Horticulture Research, 9. doi: 10.1093/HR/UHAC021.

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