Selective constraints in cold-region wild boars may defuse the effects of small effective population size on molecular evolution of mitogenomes

The pace of mitochondrial molecular evolution varies with seasonal migration distance

Animals that engage in long-distance seasonal migration experience strong selective pressures on their metabolic performance and life history, with potential consequences for molecular evolution. Species with slow life histories typically show lower rates of synonymous substitution (dS) than "fast" species. Previous research suggests long-distance seasonal migrants have a slower life history strategy than short-distance migrants, raising the possibility that rates of molecular evolution may covary with migration distance. Additionally, long-distance migrants may face strong selection on metabolically-important mitochondrial genes due to their long-distance flights. Using over 1,000 mitochondrial genomes, we assessed the relationship between migration distance and mitochondrial molecular evolution in 39 boreal-breeding migratory bird species. We show that migration distance correlates negatively with dS, suggesting that the slow life history associated with long-distance migration is reflected in rates of molecular evolution. Mitochondrial genes in every study species exhibited evidence of purifying selection, but the strength of selection was greater in short-distance migrants, contrary to our predictions. This result may indicate effects of selection for cold tolerance on mitochondrial evolution among species overwintering at high latitudes. Our study demonstrates that the pervasive correlation between life history and molecular evolutionary rates exists in the context of differential adaptations to seasonality.

Genetic diversity and population structure analysis of Philippine native pigs highlight five priority populations for conservation

The Philippine native pig (PhNP) is a unique genetic resource composed of multiple domesticated Sus scrofa lineages and interspecific hybrids. No prior study has determined the population structure and genetic diversity of PhNPs on multiple islands and provinces, which is essential for establishing conservation priorities. In this study, we explore the population structure and genetic diversity of various PhNP populations in Luzon and the Visayas, Philippines, to identify conservation priorities. We analyzed seven PhNP populations (n = 20-27 samples each; Benguet [B], Kalinga [K], Nueva Vizcaya [N], Isabela [I], Quezon [Q], Marinduque [M], and Samar [S]) and four transboundary breeds present in the Philippines (n = 9-11 samples each; Duroc, Large White, Landrace, and Berkshire). The pigs were compared against a panel of 20 microsatellite markers recommended by the ISAG-FAO. We tested for population structure at the island, region, and province levels. Strong genetic differentiation between native and transboundary breeds was confirmed by Bayesian clustering (k = 2) and Nei's D A genetic distance (100% bootstrap support for the PhNP cluster). PhNP exhibited high heterozygosity (Ho: 0.737), a high allele count (Na: 7.771), and a low inbreeding coefficient (Fis: -0.040-0.125). Bayesian clustering supported genetic differentiation at the island (k = 2; North Luzon and South Luzon-Visayas cluster), region (k = 3), and population (k = 8) levels. The pairwise F'st between PhNP populations ranged from 0.084 (N and I) to 0.397 (Q and K), confirming that some PhNP populations exhibited sufficient genetic distance to be considered separate populations. This study shows that native pigs from B, K, I, Q, M, and S are unique genetic units for conservation. Furthermore, the small effective population sizes of B, I, Q, M, and S (Ne: 3.9, 19.1, 14.2, 44.7, and 22.5, respectively) necessitate immediate conservation actions, such as incentivizing PhNP farming.

A Comprehensive Analysis of the Fowleria variegata (Valenciennes, 1832) Mitochondrial Genome and Its Phylogenetic Implications within the Family Apogonidae

Controversies surrounding the phylogenetic relationships within the family Apogonidae have persisted due to the limited molecular data, obscuring the evolution of these diverse tropical marine fishes. This study presents the first complete mitochondrial genome of Fowleria variegata, a previously unrepresented genus, using high-throughput Illumina sequencing. Through a comparative mitogenomic analysis, F. variegate was shown to exhibit a typical genome architecture and composition, including 13 protein-coding, 22 tRNA and 2 rRNA genes and a control region, consistent with studies of other Apogonidae species. Nearly all protein-coding genes started with ATG, while stop codons TAA/TAG/T were observed, along with evidence of strong functional constraints imposed via purifying selection. Phylogenetic reconstruction based on maximum likelihood and Bayesian approaches provided robust evidence that F. variegata forms a basal lineage closely related to P. trimaculatus within Apogonidae, offering novel perspectives into the molecular evolution of this family. By generating new mitogenomic resources and evolutionary insights, this study makes important headway in elucidating the phylogenetic relationships and mitogenomic characteristics of Apogonidae fishes. The findings provide critical groundwork for future investigations into the drivers of diversification, speciation patterns, and adaptive radiation underlying the extensive ecological diversity and biological success of these marine fishes using phylogenomics and population genomics approaches.

Characterization of Growth Secondary Hair in Min Pig Activated by Follicle Stem Cell Stimulated by Wnt and BMP Signaling Pathway

In China, the national-level protected pig, the Min pig, is characterized by the development of secondary hairs and hair follicles in winter. Factors that dominate the genotype in the growth of secondary hairs are not clear through the concrete cell signaling pathways. This study compared hair phenotypes based on morphological structure, transcriptomics, and potential targeting molecules in the breeds of Min, Berkshire, and Yorkshire pigs. The results indicated that Min pigs have specific characteristics for the growth of secondary hairs compared with the Berkshire and Yorkshire pigs. The transcriptome analyses and quantitative reverse transcription-polymerase chain reaction results revealed that secondary hair growth was activated by follicle stem cells. The specific inhibitors of Wnt and BMP were studied using respective signals. The density of follicles, activity of follicle stem cells, and relative gene expression results have shown that Wnt and BMP stimulate the activity of follicle stem cells, and the Wnt signaling molecule has a significantly better effect than the BMP signaling molecule on stem cells. Wnt and BMP can promote the growth of local secondary hair and gene expression. Therefore, this study was conducted to verify the development mechanisms of secondary hairs, which have potential applications in laboratory animals and comparative medicine.

The de novo assembly of a European wild boar genome revealed unique patterns of chromosomal structural variations and segmental duplications

The rapid progress of sequencing technology has greatly facilitated the de novo genome assembly of pig breeds. However, the assembly of the wild boar genome is still lacking, hampering our understanding of chromosomal and genomic evolution during domestication from wild boars into domestic pigs. Here, we sequenced and de novo assembled a European wild boar genome (ASM2165605v1) using the long‐range information provided by 10× Linked‐Reads sequencing. We achieved a high‐quality assembly with contig N50 of 26.09 Mb. Additionally, 1.64% of the contigs (222) with lengths from 107.65 kb to 75.36 Mb covered 90.3% of the total genome size of ASM2165605v1 (~2.5 Gb). Mapping analysis revealed that the contigs can fill 24.73% (93/376) of the gaps present in the orthologous regions of the updated pig reference genome (Sscrofa11.1). We further improved the contigs into chromosome level with a reference‐assistant scaffolding method. Using the ‘assembly‐to‐assembly’ approach, we identified intra‐chromosomal large structural variations (SVs, length >1 kb) between ASM2165605v1 and Sscrofa11.1 assemblies. Interestingly, we found that the number of SV events on the X chromosome deviated significantly from the linear models fitting autosomes (R² > 0.64, p < 0.001). Specifically, deletions and insertions were deficient on the X chromosome by 66.14 and 58.41% respectively, whereas duplications and inversions were excessive on the X chromosome by 71.96 and 107.61% respectively. We further used the large segmental duplications (SDs, >1 kb) events as a proxy to understand the large‐scale inter‐chromosomal evolution, by resolving parental‐derived relationships for SD pairs. We revealed a significant excess of SD movements from the X chromosome to autosomes (p < 0.001), consistent with the expectation of meiotic sex chromosome inactivation. Enrichment analyses indicated that the genes within derived SD copies on autosomes were significantly related to biological processes involving nervous system, lipid biosynthesis and sperm motility (p < 0.01). Together, our analyses of the de novo assembly of ASM2165605v1 provides insight into the SVs between European wild boar and domestic pig, in addition to the ongoing process of meiotic sex chromosome inactivation in driving inter‐chromosomal interaction between the sex chromosome and autosomes.

Correlation of the iron level in the bristles of Kemerovo pigs with macro- and essential microelements

Correlation data analysis of the iron content with macro- and essential microelements, as well as on the group of chemical elements interrelated with the Fe level in pig bristles are presented. The studies were carried out of the Kemerovo region on six-month-old pigs of the Kemerovo breed. Chemical analysis of swine bristle samples was carried out using atomic absorption spectrometry. The data were processed using of the program R. Only positive relationships were established between the iron content and the chemical elements of the bristle, as well as the group of chemical elements associated with the Fe level in the bristle. Most of the connections are explained by comparing the data obtained with the research of other scientists on the topic.

What Do We Really Know About Adaptation at Range Edges?

Recent theory and empirical evidence have provided new insights regarding how evolutionary forces interact to shape adaptation at stable and transient range margins. Predictions regarding trait divergence at leading edges are frequently supported. However, declines in fitness at and beyond edges show that trait divergence has sometimes been insufficient to maintain high fitness, so identifying constraints to adaptation at range edges remains a key challenge. Indirect evidence suggests that range expansion may be limited by adaptive genetic variation, but direct estimates of genetic constraints at and beyond range edges are still scarce. Sequence data suggest increased genetic load in edge populations in several systems, but its causes and fitness consequences are usually poorly understood. The balance between maladaptive and positive effects of gene flow on fitness at range edges deserves further study. It is becoming increasingly clear that characterizations about degree of adaptation based solely on geographical peripherality are unsupported.

Genetic analysis of whole mitochondrial genome of Lateolabrax maculatus (Perciformes: Moronidae) indicates the presence of two populations along the Chinese coast

The whole mitochondrial genome ofLateolabrax maculatus(Cuvier, 1828) was used to investigate the reasons for the observed patterns of genetic differentiation among 12 populations in northern and southern China. The haplotype diversity and nucleotide diversity ofL. maculatuswere 0.998 and 0.00169, respectively. Pairwise FSTvalues between populations ranged from 0.001 to 0.429, correlating positively with geographic distance. Genetic structure analysis and haplotype network analysis indicated that these populations were split into two groups, in agreement with geographic segregation and environment. Tajima’s D values, Fu’s Fs tests and Bayesian skyline plot (BSP) indicated that a demographic expansion event may have occurred in the history ofL. maculatus. Through selection pressure analysis, we found evidence of significant negative selection at the ATP6, ND3, Cytb, COX3, COX2 and COX1 genes. In our hypotheses, this study implied that demographic events and selection of local environmental conditions, including temperature, are responsible for population divergence. These findings are a step forward toward the understanding of the genetic basis of differentiation and adaptation, as well as conservation ofL. maculatus.

Where winter rules: Modeling wild boar distribution in its north-eastern range

Wild boars are distributed almost all over the Earth. Though, Northern Asia remained not inhabited by the species until the end of the 20th century. In the last two decades slowly but surely the wild boar has expanded the northeastern edge of its range to the northern border of the taiga. Investigating environmental factors that underlie range expansions is crucial for understanding its mechanism and predict future changes in species distribution and biodiversity. Here we investigated the distribution of wild boar in its northeastern range, comparing the role of habitat and climate variables at three spatial scales: the permanently occupied area, the area of potential expansion and the total area. We have shown that along the gradient of wild boar occupancy (from permanently to sporadically occupied to presently unoccupied) the importance of habitat variables decreases while importance of climatic variables increases. Our analysis suggests that the potential range increase of the species results from the combined effect of habitat and climatic variables. A possibility for future expansion, however, is rather related to climate change (particularly to the increase of temperature at high latitudes) than to the alteration of habitat or shifts in resource use.

Maternal genomic variability of the wild boar (Sus scrofa) reveals the uniqueness of East-Caucasian and Central Italian populations

The phylogeography of the European wild boar was mainly determined by postglacial recolonization patterns from Mediterranean refugia after the last ice age. Here we present the first analysis of SNP polymorphism within the complete mtDNA genome of West Russian (n = 8), European (n = 64), and North African (n = 5) wild boar. Our analyses provided evidence of unique lineages in the East-Caucasian (Dagestan) region and in Central Italy. A phylogenetic analysis revealed that these lineages are basal to the other European mtDNA sequences. We also show close connection between the Western Siberian and Eastern European populations. Also, the North African samples were clustered with the Iberian population. Phylogenetic trees and migration modeling revealed a high proximity of Dagestan sequences to those of Central Italy and suggested possible gene flow between Western Asia and Southern Europe which was not directly related to Northern and Central European lineages. Our results support the presence of old maternal lineages in two Southern glacial refugia (i.e., Caucasus and the Italian peninsula), as a legacy of an ancient wave of colonization of Southern Europe from an Eastern origin.