Body Size Traits Research Articles

Trait evolution and historical biogeography shape assemblages of annual killifish

AbstractAimDifferent species assemblages of annual killifish possess replicated body size distributions yet have unique sets of species in each area of endemism. Here, we use models of trait evolution and historical biogeography to discover how size variation originated and has been restructured.LocationSouth America.TaxonAustrolebias (Cyprinodontiformes).MethodsWe sampled 63 individuals from 26 Austrolebias species. Using phylogenetic trees (BEAST2), data on environmental variables at sampling locations and size data, we compare different models for trait evolution (SURFACE, l1OU) of body size and niche traits. We model the historical biogeography of the areas of endemism (BioGeoBEARS) and use both analyses in combination to reconstruct the history of four species assemblages.ResultsWe present new phylogenetic trees for Austrolebias and use them to show that large size principally arose within a single area driven by a shifted selection optimum for a subset of the species in that area. We suggest that ecological interactions triggered size divergence and that this large‐bodied lineage subsequently spread to two other areas. A second assemblage may have been shaped by adaptation to a new environment without an associated increase in size divergence. A third assemblage, which has the smallest size range and the most recent origin, is phylogenetically clustered, and we found no evidence of environmental filtering.Main conclusionsAssemblage similarity in Austrolebias is the result of contrasting ecological, evolutionary and historical processes. Modelling trait evolution together with historical biogeography can help to disentangle the complex histories of multispecies assemblages. This approach provides context to commonly used tests investigating the role of ecological processes from phylogenetic data and generates new testable hypotheses on the processes that generated trait diversity and assemblage similarity.

Genetic parameters for ultrasound-evaluated carcass and body traits in Anglo-Nubian goats

Background: Meat goat breeding programs should prioritize the identification and selection of genetically superior animals for traits related to meat quality and carcass yield in order to increase the value of the final product. Objective: To estimate (co)variance components and genetic parameters for ultrasound-measured carcass traits, body size and body weight in AngloNubian breed goats raised in the Mid-North region of Brazil. Methods: (Co)variance components and genetic parameters were estimated using the single and two-trait animal model analyses via Bayesian inference for loin eye dimensions (area, length, and depth), sternal fat thickness, rump height, chest circumference and depth, leg perimeter, and body weight. Results: Heritability estimates were higher when two-trait analyses were used. This finding implies that it is possible to recover part of the additive genetic variance included in the residual variance due to the correlation between traits. Genetic correlations between carcass and body size traits showed different magnitudes. On the other hand, genetic correlations between the traits related to muscularity showed high magnitudes. Conclusions: Body weight was not a good indicator of muscularity; therefore, it is not recommended as a criterion for indirect selection to improve carcass traits of Anglo-Nubian goats. Leg perimeter and chest circumference may be important to construct selection indexes in meat goat breeding programs.

Relationship between body size traits and carcass traits with primal cuts yields in Hanwoo steers.

ObjectiveThis study was conducted to evaluate the correlation between body size traits, carcass traits, and primal cuts in Hanwoo steers.MethodsSixty-one beef carcasses were classified for conformation and primal cut weight. Additionally, carcass weight, fat thickness, carcass dimensions, and longissimus muscle area were determined to complement the grading.ResultsThe average live weight and cold carcass weight were 759 and 469 kg, respectively. The mean carcass meat, fat, and bone proportions were 551, 298, and 151 g/kg, respectively. Primal cuts weights showed significant positive correlations (p<0.001) of 0.42 to 0.82 with live weight, carcass weight, and longissimus muscle area and a significant negative correlation with carcass fat (without shank, −0.38 to −0.10). Primal cut weights were positively correlated (p<0.01) with carcass length (0.41 to 0.77), forequarter length (0.33 to 0.57), 6th lumbar vertebrae–heel length (0.33 to 0.59), 7th cervical vertebrae carcass breadth (0.35 to 0.58), 5th to 6th thoracic vertebrae breadth (0.36 to 0.65), 7th to 8th thoracic vertebrae girth (0.38 to 0.63), and coxae girth (0.34 to 0.56) and non-significantly related to cervical vertebrae length and coxae thickness.ConclusionThere was a high correlation among live weight, carcass weight, longissimus muscle area, carcass length, 7th cervical vertebrae carcass breadth, 5th to 6th thoracic vertebrae breadth, and 7th to 8th thoracic vertebrae girth of the primal cuts yield. The correlation between fat and primal cut yields was highly significant and negative. Carcass length and 7th to 8th thoracic vertebrae girth, appear to be the most important traits affecting primal cut yields.

Urbanisation and Fishing Alter the Body Size and Functional Traits of a Key Fisheries Species

Human pressures on ecosystems from landscape transformation and harvesting can result in changes to body size and functional traits of affected species. However, these effects remain very poorly understood in many settings. Here we examine whether and how fishing and the attributes of coastal seascapes can operate in concert to change the body size and functional traits of the giant mud crab, Scylla serrata; a prized fisheries species. We captured 65 legal sized (> 15 cm carapace width) male giant mud crabs from 13 estuaries in southeast Queensland, Australia. These estuaries span a wide range of fishing and catchment landscape transformation intensity. We made a total of 9000 external morphometric measurements in the study. There was a distinct effect of estuarine landscape context on body size, with the largest individuals captured from systems with bigger inlets and lower extent of intertidal flats. Variation in functional traits was most often associated with variation in fishing pressure and human population size in the catchment. Crabs from areas with less commercial fishing pressure and lower human populations in the catchment had the largest chelipeds. We also found effects of urbanisation (negative correlations), intertidal flats (inconsistent effects) and mangrove extent (positive correlations) on the size of some functional traits. Our results show that human pressures can have sublethal effects on animals in estuaries that alter body size and functional traits. These phenotypic responses might have consequences for the fitness and ecological roles of targeted species, and the yields of fisheries catches.

Allometry in an eco-evolutionary network model

An eco-evolutionary food web model is modified to incorporate a body-size trait, enabling a framework for non-uniform mortality and ecological efficiency between species. Evolved communities feature increased connectance, with according benefits to community robustness, and persistent top predators but reduced omnivory and food chain lengths. Body-size maintains a strong positive correlation to trophic level, but does not correlate to an individual species’ contribution to network stability. A spatially-explicit extension of the model assembles large metacommunities with distinct distributions of body-size amongst local food webs.

The scaling of biomass variance across trophic levels in stream species communities: a macroecological approach

Much has been published about different aspects of body-size distribution resting on the assumptions of metabolic scaling, although a number of studies in aquatic ecosystems have questioned its generality. This study considers the effects of individual body-mass and biomass variability on scaling properties of multi-species communities (protists, meio- and macroinvertebrates), and their intrinsic variations in assemblage structure. We examine how size traits within communities are distributed on local and regional scales and assess the potential sources of variation affecting whole ecosystems. Our results, built upon seven river catchment communities including 1204 species, revealed micro-meiofauna-dominated biomass distributions driven by stochastic hydrophysical processes that induce a fractal fluctuation scaling, irrespective of trophic levels, shaping local and regional scaling relations. Fractal-scaling differences are largely generated by the frequency of high flow events that influence the biomass assemblage configurations, which are significantly better represented by the Power Fraction model compared to single statistical random models. We conclude that environmental random variability contributes to the decoupling of total biomass and body mass per site from assemblage size, resulting in scale-invariant body-size traits among assemblages and systems. Generally, these findings emphasize that ignoring small-sized species and, thus, the wide range of body sizes makes accurate ecological model predictions, impossible.

Copy Number Variation of the PIGY Gene in Sheep and Its Association Analysis with Growth Traits.

Simple SummaryThe PIGY (phosphatidylinositol glycan anchor biosynthesis class Y) gene is a member of the PIG gene family and encodes the glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex. It initiates the biosynthesis of GPI and plays an important role in cell–cell interactions. Sequencing has revealed a 3600 bp copy number variation (CNV) in exon 2 of the PIGY gene in sheep, potentially altering a functional part of the protein. The CNV overlaps 28 quantitative trait loci that are relevant to some economic traits like muscle density and carcass weight. We screened for this CNV of the PIGY gene in 569 individuals, namely, 240 Chaka sheep (CKS), 168 Hu sheep (HS), and 161 small-tailed Han sheep (STHS), and analyzed the association between the presence of this CNV and sheep body size traits. The results showed that the loss-type CNV was more prevalent than other types in these three breeds, and there were significant effects of the PIGY gene CNV on body weight, chest circumference, and circumference of cannon bone of sheep. The results showed that sheep with gain-type CNV had better growth traits than those with other types. The findings reveal the relationship between the CNV of the PIGY gene and growth traits of sheep, suggesting that CNV could be utilized for improved molecular breeding of sheep.Copy number variation (CNV) is a type of genomic variation with an important effect on animal phenotype. We found that the PIGY gene contains a 3600 bp copy number variation (CNV) region located in chromosome 6 of sheep (Oar_v4.0 36,121,601–36,125,200 bp). This region overlaps with multiple quantitative trait loci related to phenotypes like muscle density and carcass weight. Therefore, in this study, the copy number variation of the PIGY gene was screened in three Chinese sheep breeds, namely, Chaka sheep (CKS, May of 2018, Wulan County, Qinghai Province, China), Hu sheep (HS, May of 2015, Mengjin County, Henan Province, China), and small-tailed Han sheep (STHS, May of 2016, Yongjing, Gansu Province, China). Association analyses were performed on the presence of CNV and sheep body size traits. We used real-time quantitative PCR (qPCR) to detect the CNV for association analysis. According to the results, the loss-type CNV was more common than other types in the three breeds (global average: loss = 61.5%, normal = 17.5%, and gain = 21.0%). The association analysis also showed significant effects of the PIGY gene CNV on body weight, chest circumference, and circumference of the cannon bone of sheep. Sheep with gain-type CNV had better growth traits than those with other types. The results indicate a clear relationship between the PIGY gene CNV and growth traits of sheep, suggesting the use of CNV as a new molecular breeding marker.

Polymorphism of VRTN Gene g.20311_20312ins291 Was Associated with the Number of Ribs, Carcass Diagonal Length and Cannon Bone Circumference in Suhuai Pigs.

Simple SummaryAn increase in the number of ribs (RIB) could improve carcass length (CL) and body size. Cannon bone circumference (CBC) is a pivotal body size trait, and a large CBC could enhance the capacity to bear excessive body weight, vigorous exercise, and resistance to injuries. Several researchers showed that the vertnin (VRTN) gene g.20311_20312ins291 (NC_010449.5 7: g.20311_20312ins291) is an important variant that is related to RIB and CL of Western pigs. However, it is unknown whether this variant could affect the CBC of pigs. Our study showed that this variant was significantly associated with RIB, carcass diagonal length (CDL), and CBC in Suhuai pigs; therefore, it could be used as a potential molecular marker for improving RIB, CDL, and CBC in this breed.The vertnin (VRTN) gene g.20311_20312ins291 was reported as an important variant related to the number of ribs (RIB), and the ins/ins genotype was advantageous for improving RIB of Western pigs. The purpose of this study was to determine whether the VRTN gene g.20311_20312ins291 influences RIB, carcass traits, and body size traits, including cannon bone circumference (CBC) in Chinese Suhuai pigs. We found that the VRTN gene g.20311_20312ins291 was polymorphic in Suhuai fattening pigs and gilts. The polymorphism of g.20311_20312ins291 was significantly associated with RIB and CDL in Suhuai fattening pigs (p < 0.01), whereas this variant had no influence on carcass weight (CWT). There was a tendency of association between this variant and carcass straight length (CSL) in Suhuai fattening pigs (p = 0.06). The polymorphism of g.20311_20312ins291 was also significantly associated with CBC in Suhuai gilts (p = 0.04). Furthermore, CBC was positively genetically correlated with body length (0.22, p < 0.01) and body weight (0.15, p < 0.01). Our results indicated that the VRTN gene g.20311_20312ins291 could be used as a potential marker for improving RIB, CDL, and CBC in Suhuai pigs.

Bioinformatics analysis and genetic polymorphisms in genomic region of the bovine SH2B2 gene and their associations with molecular breeding for body size traits in qinchuan beef cattle.

The Src homology 2 B 2 (SH2B2) gene regulate energy balance and body weight at least partially by enhancing Janus kinase-2 (JAK2)-mediated cytokine signaling, including leptin and/or GH signaling. Leptin is an adipose hormone that controls body weight. The objective of the present study is to evaluate the association between body measurement traits and SH2B2 gene polymorphisms as responsible mutations. For this purpose, we selected four single-nucleotide polymorphisms (SNPs) in SH2B2 gene, including two in intron 5 (g.20545A>G, and g.20570G>A, one synonymous SNP g.20693T>C, in exon 6 and one in intron 8 (g.24070C>A, and genotyped them in Qinchuan cattle. SNPs in sample populations were in medium polymorphism level (0.250<PIC<0.500). Association study indicated that the g.20570G>A, g.20693T>C, and g.24070C>A, significantly (P < 0.05) associated with body length (BL) and chest circumference (CC) in Qinchuan cattle. In addition, H4H3 and H5H5 diplotype had highly significantly (P < 0.01) greater body length (BL), rump length (RL), and chest circumference (CC) than H4H2. Our investigation will not only extend the spectrum of genetic variation of bovine SH2B2 gene, but also provide useful information for the marker assisted selection in beef cattle breeding program.

Whole-genome analyses identify loci and selective signals associated with body size in cattle.

Body size plays a key role in production, health, selection, and environmental adaptation of animals, but the genetic basis of body size variation is not clearly understood. Here, we conducted genome-wide association studies (GWAS) of 15 body size traits using autosomal single nucleotide polymorphisms (SNPs) derived from whole-genome sequences of 31 Brahman cattle and 131 Yunling cattle and identified 20 significant loci, which implicated 18 candidate genes. For ischium width, the most significant SNP was assigned to LCORL, a famous gene controlling body size. For chest width, the most significant SNP was located upstream of BMP5, a secreted ligand of transformation growth factor-beta superfamily of proteins involved in bone and cartilage development. Subsequently, we detected selective sweeps in Brahman cattle using integrated Haplotype Score, composite likelihood ratio, and nucleotide diversity. The results showed CNTNAP5 locus associated with hip cross height and LIMCH1 locus associated with forehead size were in selective signals, which were consistent with higher hip cross height and higher forehead size in Brahman cattle compared with Yunling cattle. Our findings provide genetic insights into variation and selection of body size using GWAS and selective signals and will accelerate future efforts aimed at cattle improvement.

The geographical diversification in varanid lizards: the role of mainland versus island in driving species evolution.

Monitor lizards (Varanidae) inhabit both the mainland and islands of all geological types and have diversified into an exceptionally wide range of body sizes, thus providing an ideal model for examining the role of mainland versus island in driving species evolution. Here we use phylogenetic comparative methods to examine whether a link exists between body size-driven diversification and body size-frequency distributions in varanid lizards and to test the hypothesis that island lizards differ from mainland species in evolutionary processes, body size, and life-history traits (offspring number and size). We predict that: 1) since body size drives rapid diversification in groups, a link exists between body size-driven diversification and body size-frequency distributions; 2) because of various environments on island, island species will have higher speciation, extinction, and dispersal rates, compared with mainland species; 3) as a response to stronger intraspecific competition, island species will maximize individual ability associated with body size to outcompete closely-related species, and island species will produce smaller clutches of larger eggs to increase offspring quality. Our results confirm that the joint effect of differential macroevolutionary rates shapes the species richness pattern of varanid lizards. There is a link between body size-driven diversification and body size-frequency distributions, and the speciation rate is maximized at medium body sizes. Island species will have higher speciation, equal extinction, and higher dispersal rates compared with mainland species. Smaller clutch size and larger hatchling in the island than in mainland species indicate that offspring quality is more valuable than offspring quantity for island varanids.

Genetic relationships of calving difficulty with birth measurements and carcass traits in Japanese Black cattle.

The objectives of this study were to compare the genetic parameters for calving difficulty (CD), which were treated as both a calf trait (CD_calf) and as a dam trait (CD_dam), and to clarify genetic relationships of these CDs with body size traits of calves at birth and carcass traits. In total, the CD records and calf body measurements of 2,258 Japanese Black cattle heifers were used in this study, in addition to the carcass records of 4,300 feedlot steers and heifers. Direct heritability of CD_calf (0.44) was higher than maternal heritability of CD_calf (0.30), as well as CD_dam heritability (0.25). Direct genetic correlations between CD_calf and calf body size were moderate to strongly positive (0.64 to 0.81). The correlations between EBVs of CDs and carcass weight were also positive (0.30 to 0.64). These positive relationships showed that genetically improving CD (reducing dystocia) could produce smaller calves and carcasses. In contrast, the correlations between CDs and beef marbling score were weak, suggesting that improving CD would not influence meat quality traits. Fitting an animal model to CD_calf could be more preferred to fitting the model to CD_dam, because the former could separate the genetic effects of dams and calves.

Hierarchical analysis of wild Atlantic salmon (Salmo salar) fecundity in relation to body size and developmental traits.

Using data from wild Atlantic salmon Salmo salar returning to spawn in seven Scottish rivers, we developed a model of fecundity based on individual body size and key developmental traits. We used a novel approach to model selection which maximises predictive accuracy for application to target river stocks to select the best from a suite of Bayesian hierarchical models. This approach aims to ensure the optimal model within the candidate set includes covariates that best predict out-of-sample data to estimate fecundity in areas where no direct observations are available. In addition to body size, the final model included the developmental characteristics of age at smolting and years spent at sea. Using two independent long-term monitoring datasets, the consequences of ignoring these characteristics was revealed by comparing predictions from the best model with models that omitted them.

Are macroinvertebrate traits reliable indicators of specific agrichemicals?

Abstract Determining the extent of freshwater contamination by agrichemicals is a major challenge. Biological indicators have been proposed as indirect measures of contaminants that can be used to reduce chemical monitoring costs by identifying pollution hotspots that warrant thorough chemical testing. Many general indicators are based on taxonomic properties of aquatic macroinvertebrate communities. However, it has been suggested that metrics based on traits, rather than taxa, can be used to develop more chemical-specific and efficient indicators. Here, we investigate whether macroinvertebrate family-level traits can be used as simple indicators of elevated levels of specific pollutants in farmland drainage ditches, to reveal areas in need of further chemical monitoring. We selected seven traits—body size, body armouring, feeding guild, habit, oxygen acquisition, dispersal mode, and voltinism—that we predicted would influence sensitivity to nitrate, to the two herbicides atrazine and glyphosate, and to neonicotinoid insecticides, and tested whether any trait-chemical relationships were strong enough to be reliable bioindicators. We collected macroinvertebrate samples and water samples for agrichemical analyses from 27 farmland ditches in Eastern Ontario, Canada. We indexed the sensitivity of each sampled macroinvertebrate family to the concentration of each agrichemical, using coefficients from multiple logistic regressions of family absence/presence on the concentrations of the four agrichemicals. We reduced the seven traits predicted to influence sensitivity to four—body armouring, oxygen acquisition, dispersal mode, and voltinism—after examining their inter-dependencies. We then tested for cross-family relationships between sensitivity to each chemical and the trait categories for each macroinvertebrate family. Two traits, oxygen acquisition and dispersal mode, were significantly associated with two agrichemical sensitivity coefficients: nitrate sensitivity was associated with mode of oxygen acquisition, with atmospheric breathers having a higher mean sensitivity coefficient than dissolved-oxygen breathers, and glyphosate sensitivity was related to dispersal mode, with passive dispersers having a higher mean sensitivity coefficient than active dispersers. However, inspection of these relationships revealed that the responses lacked enough consistency across families to be reliable, chemical-specific indicators. Instead, a taxa-level, post-hoc analysis indicated that further work should be conducted to determine whether there are individual taxa whose presence at a site is a strong indicator of a lack or low levels of certain contaminants. In particular, the presence of Corixidae appears to indicate low ditch nitrate levels. Overall, however, our results combined with previous work suggest that we are unlikely to find chemical-specific macroinvertebrate indicators that are more efficient than a rigorous chemical sampling scheme.

The Distribution Characteristics of a 19-bp Indel of the PLAG1 Gene in Chinese Cattle.

Simple SummaryGrowth traits are important quantitative traits for cattle performance, which influences herd productivity. Previous studies demonstrated that a 19-bp indel in pleomorphic adenoma gene 1 (PLAG1) is associated with bovine growth traits. In our studies, the distribution of the 19-bp indel of PLAG1 gene among 37 Chinese cattle breeds and the association between this indel and growth traits of Yunling cattle were explored. As a result, we found that the average body height of various Chinese cattle breeds showed an increasing trend from south to north of China, which was consistent with the distribution trend of the 19-bp indel in cattle at different geographic latitudes. Moreover, this indel was verified to be significantly associated with the growth traits of Yunling cattle. Our results showed that the 19-bp indel in PLAG1 strongly influences body size in Chinese cattle.Pleomorphic adenoma gene 1 (PLAG1) belongs to the PLAG family of zinc finger transcription factors. In cattle, a 19-bp insertion/deletion (indel) was identified in intron 1 of the PLAG1 gene (GenBank Accession No. AC_000171.1). Researches showed that the indel is polymorphic in Chinese cattle breeds such as Qinchuan cattle, Pinan cattle, Xianan cattle, and Jiaxian red cattle, and correlation analysis showed that the polymorphism is related to the height of these cattle breeds. Chinese cattle breeds show a difference in height related to geographical distribution. We investigated the distribution of the 19-bp indel polymorphism in 37 cattle breeds, including 1354 individuals. The results showed that there were three genotypes and two alleles (W, 366 bp; D, 347 bp). From northern cattle to southern cattle, the frequency of W allele gradually decreased, while the frequency of D allele showed an opposite trend, which was consistent with the distribution of cattle breeds of different height in China. Therefore, the polymorphism of this indel may be related to the regional distribution of cattle breeds in China. In addition, we chose Yunling cattle with a mixed genetic background to study the genetic effects of the 19-bp indel on body size traits. Statistical analysis showed that PLAG1 was significantly associated with the body height, cross height, and chest circumference of Yunling cattle (p < 0.05). This study provides new evidence that the 19-bp indel of the PLAG1 gene is a highly effective trait marker that can be used as a candidate molecular marker for cattle breeding.

131 Genetic variants and haplotype combination in the bovine SH2B2 gene and their associations with molecular breeding for body size traits in Qinchuan cattle (Bos taurus)

The Src homology 2B 2 (SH2B2) gene regulates energy balance and body weight at least partially by enhancing Janus kinase-2 (JAK2)-mediated cytokine signalling, including leptin or GH signalling. Leptin is an adipose hormone that controls body weight. The objective of the current study was to evaluate the association between body measurement traits and SH2B2 gene polymorphisms. For this purpose, we selected four single-nucleotide polymorphisms (SNPs) in the SH2B2 gene, including two in intron 5 (A20545G and G20570A), one synonymous SNP (T20693C) in exon 6, and one in intron 8 (C24070A), and genotyped these through DNA sequencing in Qinchuan cattle. The general linear model (GLM) in SPSS 20.0 software (SPSS Inc.) was used for the association analysis between SNPs and selected traits of carcass quality. The SNPs in sample populations were in medium polymorphism level (0.250&amp;lt;pic&amp;lt;0.500). This association study indicated that the G20570A, T20693C, and C24070A were significantly (P&amp;lt;0.05) associated with body length (BL) and chest circumference (CC) in Qinchuan cattle. In addition, the H4H3 and H5H5 diplotype were associated with significantly (P=0.01) greater BL and rump length than was H4H2. Our investigation will not only extend understanding of genetic variations in the bovine SH2B2 gene but also provide useful information for marker-assisted selection in beef cattle breeding programs.

Evolution of cis- and trans-regulatory divergence in the chicken genome between two contrasting breeds analyzed using three tissue types at one-day-old

BackgroundGene expression variation is a key underlying factor influencing phenotypic variation, and can occur via cis- or trans-regulation. To understand the role of cis- and trans-regulatory variation on population divergence in chicken, we developed reciprocal crosses of two chicken breeds, White Leghorn and Cornish Game, which exhibit major differences in body size and reproductive traits, and used them to determine the degree of cis versus trans variation in the brain, liver, and muscle tissue of male and female 1-day-old specimens.ResultsWe provided an overview of how transcriptomes are regulated in hybrid progenies of two contrasting breeds based on allele specific expression analysis. Compared with cis-regulatory divergence, trans-acting genes were more extensive in the chicken genome. In addition, considerable compensatory cis- and trans-regulatory changes exist in the chicken genome. Most importantly, stronger purifying selection was observed on genes regulated by trans-variations than in genes regulated by the cis elements.ConclusionsWe present a pipeline to explore allele-specific expression in hybrid progenies of inbred lines without a specific reference genome. Our research is the first study to describe the regulatory divergence between two contrasting breeds. The results suggest that artificial selection associated with domestication in chicken could have acted more on trans-regulatory divergence than on cis-regulatory divergence.

Whole Genome Resequencing Reveals Selection Signatures Associated With Important Traits in Ethiopian Indigenous Goat Populations.

Ethiopia is considered as the main gateway for the introduction of livestock species, including goat, to the African continent. Ethiopian goats are characterized by their unique adaptive ability, and different physical characteristics in terms of morphology, body size, coat colors, and other important traits. The comparative population genomic analysis provides useful genomic information associated with important traits. Whole-genome resequencing of 44 Ethiopian indigenous goats produced 16 million single-nucleotide polymorphisms (SNPs) as well as 123,577 insertions and deletions. Specifically, 11,137,576, 10,760,581, 10,833,847, 12,229,657 and 10,749,996 putative SNPs were detected in Abergelle, Afar, Begait, Central Highland and Meafure goat populations, respectively. In this study, we used population differentiation (FST) and pooled heterozygosity (HP) Cbased approaches. From the FST analysis, we identified 480 outlier windows. The HP approach detected 108 and 205 outlier windows for Abergelle, and Begait, respectively. About 11 and 5 genes under selective signals were common for both approaches that were associated with important traits. After genome annotation, we found 41 Gene ontology (GO) terms (12 in biological processes, 8 in cellular components and 11 in the molecular function) and 10 Kyoto Encyclopedia of Genes and Genomes pathways. Several of the candidate genes are involved in the reproduction, body weight, fatty acids, and disease related traits. Our investigation contributes to deliver valuable genetic information and paves the way to design conservation strategy, breed management, genetic improvement, and utilization programs. The genomic resources generated in the study will offer an opportunity for further investigations.

Expression Analysis of the PITX2 Gene and Associations between Its Polymorphisms and Body Size and Carcass Traits in Chickens.

Simple SummaryThe Wuliang Mountain Black-bone chicken is a Chinese indigenous breed with good meat quality and strong resistance to disease. Like most of the other Chinese domestic breeds, it has a much slower early growth rate compared with foreign chicken breeds. Therefore, the genetic selection of body size and carcass traits is still the focus of Chinese indigenous chicken breeding. The paired-like homeodomain transcription factor 2 (PITX2) gene, an important transcription factor, plays an important role during the development of the eye, heart, skeletal muscle and other tissues in mammals. In chicken, the PITX2 gene affects the late myogenic differentiation of the limb. The objectives of this study were to detect the expression of the PITX2 gene and analyze the associations between the polymorphisms in the exons of the PITX2 gene and body size as well as carcass traits in chickens. The results could contribute to Chinese chicken breeding based on marker assisted-selection.PITX2 is expressed in and plays an important role in myocytes of mice, and it has effects on late myogenic differentiation in chickens. However, the expression profile and polymorphisms of PITX2 remain unclear in chickens. Therefore, the aim of the present study was to detect its expression and investigate single nucleotide polymorphisms (SNPs) within its exons and then to evaluate whether these polymorphisms affect body size as well as carcass traits in chickens. The expression analysis showed that the expression level of chicken PITX2 mRNA in the leg muscle and hypophysis was significantly higher (p < 0.01) than those in other tissues. The results of polymorphisms analysis identified two SNPs (i.e., g.9830C > T and g.10073C > T) in exon 1 and 10 SNPs (i.e., g.12713C > T, g.12755C > T, g.12938G > A, g. 3164C > T, g.13019G > A, g.13079G > A, g.13285G > A, g.13335G > A, g.13726A > G and g.13856C > T) in exon 3, including four novel SNPs (i.e., g.9830C > T, g.12713C > T, g.12938G > A and g.13856C > T). In the loci of g.10073C > T and g.12713C > T, chickens with the CT genotype had the highest (p < 0.05 or p < 0.01) breast depth and breast angle, respectively. For the locus of g.13335G > A, chickens with the GG genotype had the highest (p < 0.05 or p < 0.01) breast angle and shank circumference. For the locus of g.13726A > G, chickens with the GG genotype had the highest breast width, fossil keel bone length and shank circumference. The locus of g.12713A > G had significant effects on the PITX2 mRNA expression level in leg muscle. The H1H7 diplotype showed the highest shank circumference, and the H2H8 diplotype showed the highest breast muscle rate. The present research suggested that polymorphisms of the exons of the PITX2 gene were significantly associated with the body size and carcass traits of Wuliang Mountain Black-bone chickens and the PITX2 gene could be a potential candidate gene for molecular marker-aided selection in Wuliang Mountain Black-bone chickens and other chicken breeds.

Lower elevation animal species do not tend to be better competitors than their higher elevation relatives

AbstractAimWhat factors set species' range edges? One general hypothesis, often attributed to Darwin and MacArthur, is that interspecific competition prevents species from inhabiting the warmest portions along geographic gradients (i.e., low latitudes or low elevations). A prediction arising from this Darwin–MacArthur hypothesis is that lower elevation species are better competitors than related higher elevation species. An alternative prediction is that higher elevation animal taxa will tend to be better competitors because they will tend to be larger (Bergmann's rule). Here, I test these opposing predictions.LocationGlobal.Time period1971–2019.Major taxa studiedBirds, mammals, amphibians, fishes.MethodsI conducted a meta‐analysis of studies that measured pairwise behavioural aggression between species‐pairs of closely related animals where the two species inhabit divergent elevational distributions.ResultsI found that (a) interspecific aggression appears to be a reliable indicator of interspecific competition; (b) elevational position was not consistently linked to interspecific aggression—while lower elevation songbird species in the tropics showed stronger interspecific aggression in response to playback experiments, higher elevation species showed stronger interspecific aggression in direct observations of interspecific aggression across a range of taxa and latitudes; (c) body size was a good predictor of pairwise interspecific aggression and (d) there was limited evidence for Bergmann's rule.Main conclusionsMy results do not support the longstanding prediction that lower elevation animals are generally better competitors than their higher elevation relatives. Instead, patterns of interspecific aggression are linked to body size, with larger animals showing more aggression towards smaller relatives than vice versa. Hence, a trait—body size—that is idiosyncratically related to elevational position appear to determine the outcome of pairwise behavioural interactions. Last, I consider these results in the context of the hypothesis that behavioural interactions may impact rates of upslope range shifts associated with recent warming.