Genomic investigation of the Chinese alligator reveals wild‐extinct genetic diversity and genomic consequences of their continuous decline

Abstract

Critically endangered species are usually restricted to small and isolated populations. High inbreeding without gene flow among populations further aggravates their threatened condition and reduces the likelihood of their long‐term survival. Chinese alligator (Alligator sinensis) is one of the most endangered crocodiles in the world and has experienced a continuous decline over the past c. 1 million years. In order to identify the genetic status of the remaining populations and aid conservation efforts, we assembled the first high‐quality chromosome‐level genome of Chinese alligator and explored the genomic characteristics of three extant breeding populations. Our analyses revealed the existence of at least three genetically distinct populations, comprising two breeding populations in China (Changxing and Xuancheng) and one breeding population in an American wildlife refuge. The American population does not belong to the last two populations of its native range (Xuancheng and Changxing), thus representing genetic diversity extinct in the wild and provides future opportunities for genetic rescue. Moreover, the effective population size of these three populations has been continuously declining over the past 20 ka. Consistent with this decline, the species shows extremely low genetic diversity, a large proportion of long runs of homozygous fragments, and mutational load across the genome. Finally, to provide genomic insights for future breeding management and conservation, we assessed the feasibility of mixing extant populations based on the likelihood of introducing new deleterious alleles and signatures of local adaptation. Overall, this study provides a valuable genomic resource and important genomic insights into the ecology, evolution, and conservation of critically endangered alligators.

Major histocompatibility complex genomic investigation of endangered Chinese alligator provides insights into the evolution of tetrapod major histocompatibility complex and survival of critically bottlenecked species

“…With the help of genome annotation (Wan et al, 2013), we figured out this puzzle and renewed the BAC and alligator MHC-I and MHC-IIB repertoires using the RACE sequences. The results (adjacent genes, closely linked Class I and Class II subregions and gene arrangement) were also supported by the latest TGS-based genome of the Chinese alligator (Figure 6B; Yang et al, 2022). Combined with transcriptome data, the discrepant copy numbers of MHC-I and MHC-IIB genes were more accurate in our results, which were based on BAC, RACE, and manually checking.…”

“…BAC was considered the best and precise method to study gene arrangement. To analyze whether there is a mismatch or annotation mistake in the MHC region, we compared the gene annotation of this region from secondgeneration sequencing (SGS) (Illumina short read sequencing, GCA_000455745.1) and TGS [which was available during our organizing this article, (Yang et al, 2022)] with our Alsi-BAC-MHC contig (Step 3.2 in Figure 1).…”

Genomic evidence for climatic adaptation in Fejervarya multistriata

“…After measuring the genomic differentiation among populations using a sliding window analysis with a 50‐kb window sliding in steps of 10‐kb, we calculated nucleotide diversity ( π ) and quantified population genetic differentiation ( F ST ) among populations in PIXY (version 1.2.7) (Korunes & Samuk, 2021), and estimated the linkage disequilibrium (LD) levels for every population in PopLDdecay (version 3.4.1) (Yang et al., 2023). Prior to analyses, we generated a consensus sequence that was filtered, aligned and trimmed, and the filtering conditions were bi‐allelic sites with high LD ( r 2 > .1) and minor allele count (MAC < 2).…”

Haplotype-resolved chromosome-scale genomes of the Asian and African Savannah Elephants

“…Therefore, the protection and conservation of elephants has become a focus of ecological diversity efforts. In the era of transitioning from conservation genetics to conservation genomics [4][5][6][7] , high-quality reference genome is of vital importance to improve the evaluation of the full spectrum of genomic diversity, inbreeding and outbreeding depression, local adaptation and genetic loads [8][9][10][11] . Furthermore, this genome assembly will provide a valuable resource for studying the ecology and evolution of specific species 12,13 .…”