Increased phenotypic diversity in the Icelandic goat breed following population expansion

In Spain the lean percentage of pig carcasses is predicted objectively with the Fat-O-Meat’er. Changes in the pig population can affect the accuracy of a prediction formula. The aim of this study was to see whether the present Spanish equation for the Fat-O-Meat’er, that was established after a dissection trial in 1990, is still accurate, using more recent data from a dissection trial conducted in the year 2000. The root mean squared error of prediction of the present equation was calculated. Also, a new equation, obtained with the data of the 2000 trial, was compared with the present prediction equation with respect to the constant terms and coefficients. Finally, possible bias in the present formula was studied by comparing dissection results of the 2000 trial with predictions of the present Spanish equation in relation to fat and muscle depth measurements. The calculations demonstrated that the present equation is still valid to predict the lean meat percentage.

Pasteurella multocida is responsible for economically important diseases in sheep and pigs. Antimicrobial susceptibility studies are essential for initiating rational and effective empirical therapy of P. multocida infections. In this study we investigated the antimicrobial susceptibility to 18 antimicrobial agents of 156 clinical isolates of P. multocida from sheep (n = 87) and pigs (n = 69) using the microdilution method. Both sheep and pig isolates exhibited low levels of resistance (≤ 15%) to ceftiofur, gentamicin, neomycin, spectinomycin, chlortetracycline, tulathromycin, florfenicol, danofloxacin, and enrofloxacin and trimethoprim/sulphamethoxazole, high resistance rates (> 15% up to 50%) to oxytetracycline, tilmicosin, and tiamulin, and very high resistance rates (> 50%) to tylosin tartrate, clindamycin, and sulphadimethoxine. However, sheep isolates exhibited significantly lower percentages of resistance and lower MIC90 values (P < 0.05) than pig isolates for most of the antimicrobials tested. In addition, sheep isolates exhibited also significantly lower phenotypic antimicrobial resistance diversity (8 resistotypes vs. 30 resistotypes). LAC-LIN-SUL-MAC was the resistotype most frequently detected in sheep (39.1%) and LIN-SUL-MAC in pig isolates (26.1%). The differences in susceptibility patterns could be influenced by the lower use of antimicrobials in the small ruminant industry compared with the pig farming industry.

Abstract. Asmara IY, Garnida D, Setiawan I, Partasasmita R. 2019. Short Communication: Phenotypic diversity of male pelung chickens in West Java Province, Indonesia. Biodiversitas 20: 2243-2248. Pelung chickens are indigenous chickens from Cianjur District, West Java Province, Indonesia. The male chickens have long and beautiful crowing and have a distinct body figure compared to other indigenous chickens. Chicken contests are conducted regularly as media to show singing ability and body performance of Pelung chickens. Pelung chickens raised in different areas may have different phenotypic characteristics due to keeper preferences. Also, the phenotypic characteristics of the winners of chicken contests may influence keepers to select their chickens. The objective of this study was to determine the phenotypic characteristics of male Pelung Chickens in different areas in West Java, Indonesia. Comb type, as well as the color of eye, beak, skin, plumage, and shank, were recorded in the study. Data were collected through a survey involving 160 male birds in four different districts in West Java Province including Cianjur, Sukabumi, Bandung and Garut Districts. Key informant interview was carried out to support quantitative data. The results showed a limited variation of phenotypic characteristics among male Pelung chickens. Comb type, as well as skin and plumage colors, are criteria to select male Pelung chickens. Phenotypic characteristics of contest winners are also a reference for Pelung keepers in breeding selection.

Abstract. Setianto J, Sutriyono, Prakoso H, Zain B, Adwiyansyah R, Amrullah AHK. 2019. Short Communication: Phenotypic diversity of male Burgo chicken from Bengkulu, Indonesia. Biodiversitas 20: 532-536. Burgo chicken is the result of a crossbreed of Red Junglefowl (Gallus gallus gallus) with Kampung chicken (Gallus domestica). This study aimed to describe the diversity of colors found in male Burgo chickens. The study was conducted in the city of Bengkulu, Indonesia. The method used in this study was a direct observation of the 50 male chickens on the breeders. The breeders belonging to the Burgo chicken community were determined by random sampling method. The breeders who did not join the community were determined by the snowball sampling method. This method was carried out because the presence of breeders who keep Burgo chickens was unknown. The data in this study consisted of the color of chest feathers, neck feathers, wing feathers, tail feathers, saddle feathers, and the number of wing and tail feathers. The data obtained were analyzed descriptively. The number of colors ranges 4 to 11 with the high diversity is mainly found on the feathers of the chest, neck and, saddle.

Short communication: Development and evaluation of equations to predict growth of Holstein dairy heifers in a tropical climate

Abstract. Alghozali FA, Wijayanti DP, Sabdono A. 2019. Short Communication: Genetic diversity of scalloped hammerhead sharks (Sphyrna lewini) landed in Muncar Fishing Port, Banyuwangi. Biodiversitas 20: 1154-1159. The majority of sharks caught in Indonesian fisheries were bycatch products from the tuna longline fisheries, but some regions in Indonesia fish the sharks as their main target. One of these regions is located in Muncar, Banyuwangi, which fishes the endangered Scalloped Hammerhead sharks (Sphyrna lewini) as target species. This research aimed to study the genetic diversity of the endangered Scalloped Hammerhead sharks landed in Muncar Fishing Port, Banyuwangi. Genetic analysis was done through PCR (Polymerase Chain Reaction) amplification and sequencing of the mitochondrial DNA COI (Cytochrome Oxidase subunit I) gene. Out of the 37 samples collected, 30 were successfully amplified and sequenced.The results showed moderate haplotype diversity (Hd: 0,582 ± 0,079) and low nucleotide diversity (π: 0,00392± 0,0024) with five haplotypes (h) and 26 polymorphic sites (S). Tajima’s D neutrality model values indicated a population expansion event. Two different clades were determined through phylogenetic analysis and by GenBank sequences comparison. These results provided basic information and present status of the Scalloped Hammerhead sharks population genetically within the fishing ground (Makassar Strait-Kangean Islands).

The HIV-1 epidemic in Russia is dominated by the former Soviet Union subtype A (A(FSU)) variant, but other genetic forms are circulating in the country. One is the recently described CRF63_02A1, derived from recombination between a CRF02_AG variant circulating in Central Asia and A(FSU), which has spread in the Novosibirsk region, Siberia. Here we phylogenetically analyze pol and env segments from 24 HIV-1 samples from the Novosibirsk region collected in 2013, with characterization of three new near full-length genome CRF63_02A1 sequences, and estimate the time of the most recent common ancestor (tMRCA) and the demographic growth of CRF63_02A1 using a Bayesian method. The analyses revealed that CRF63_02A1 is highly predominant in the Novosibirsk region (81.2% in pol sequences) and is transmitted both among injecting drug users and by heterosexual contact. Similarity searches with database sequences combined with phylogenetic analyses show that CRF63_02A1 is circulating in East Kazakhstan and the Eastern area of Russia bordering China. The analyses of near full-length genome sequences show that its mosaic structure is more complex than reported, with 18 breakpoints. The tMRCA of CRF63_02A1 was estimated around 2006, with exponential growth in 2008-2009 and subsequent stabilization. These results provide new insights into the molecular epidemiology, phylogeny, and phylodynamics of CRF63_02A1.

Short communication: Phenotypic and genetic diversity of wild Lactococcus lactis isolated from traditional Pecorino cheeses of Tuscany

In Estonia and Finland, 386 and 671 isolates, respectively, of Phytophthora infestans were collected during the growing seasons of 2001-2007. Collection was from groups of potato cultivars of different origin from field plots at two research institutions in eastern and northern Estonia and from variety trials at two locations and commercial potato fields in Finland. Mating type, pathotype based on virulence on a differential set of 11 R genes of Solanum demissum and response to the fungicide metalaxyl were determined in both countries by comparable methods. The diversity of the P. infestans populations in both countries over the monitoring period was high. In Finland, the proportion of A1/A2 mating types was almost equal throughout the monitoring period, while in Estonia the A1 population, dominating in 2001-2004, shifted towards an equal proportion of both mating types in 2005-2007. The diversity of the P. infestans population, as measured by virulence pathotypes and the number of avirulence factors per isolate, developed in opposite directions in Estonia and Finland from 2001-2004 to 2005-2007: the diversity decreased in Estonia and increased in Finland. Metalaxyl sensitivity in the Estonian P. infestans population increased while in Finland it decreased during the same period. Results clearly show differences between Estonian and Finnish populations of P. infestans in several aspects, which may derive from cropping practices. The high A2 mating type percentage during 2005-2007 in both countries points to soil contamination with oospores.

Role of Macrophages and Mast Cells as Key Players in the Maintenance of Gastrointestinal Smooth Muscle Homeostasis and Disease.

Objective:we present a multiscale agent-based model of Ductal Carcinoma in Situ (DCIS) in order to gain a detailed understanding of the cell-scale population dynamics, phenotypic distributions, and the associated interplay of important molecular signaling pathways that are involved in DCIS ductal invasion into the duct cavity (a process we refer to as duct advance rate here).Methods:DCIS is modeled mathematically through a hybridized discrete cell-scale model and a continuum molecular scale model, which are explicitly linked through a bidirectional feedback mechanism.Results:we find that duct advance rates occur in two distinct phases, characterized by an early exponential population expansion, followed by a long-term steady linear phase of population expansion, a result that is consistent with other modeling work. We further found that the rates were influenced most strongly by endocrine and paracrine signaling intensity, as well as by the effects of cell density induced quiescence within the DCIS population.Conclusion:our model analysis identified a complex interplay between phenotypic diversity that may provide a tumor adaptation mechanism to overcome proliferation limiting conditions, allowing for dynamic shifts in phenotypic populations in response to variation in molecular signaling intensity. Further, sensitivity analysis determined DCIS axial advance rates and calcification rates were most sensitive to cell cycle time variation.Significance:this model may serve as a useful tool to study the cell-scale dynamics involved in DCIS initiation and intraductal invasion, and may provide insights into promising areas of future experimental research.

The evolutionary drivers of genetic and phenotypic diversity in widespread Neotropical birds remain poorly understood, particularly in species with high dispersal capabilities. In this study, we examine the population genetic structure, demographic history, and phenotypic variation of Euphonia hirundinacea across its Mesoamerican range using NextRad genomic data, as well as geographic and phenotypic variables. A maximum-likelihood phylogeny confirmed the monophyly of E. hirundinacea, with two well-supported clades corresponding to geographically segregated populations that align with the subspecies E. h. hirundinacea and E. h. gnatho. Our findings indicate moderate genetic differentiation partially shaped by isolation by distance (IBD), with the Nicaragua Depression acting as a semi-permeable barrier that allows limited gene flow. Most phenotypic traits did not correlate with genetic divergence, geographic distance, or environmental variables. However, in females, wing chord and throat coloration were significantly associated with both genetic and geographic distances. Demographic analyses support a scenario of divergence initiated during Pleistocene climatic fluctuations (∼2,668,739.13 years ago), followed by population expansion during Holocene (∼20,000 years ago) and secondary contact, supported by ecological niche models. The species' ecological flexibility and high vagility likely mitigated long-term isolation and facilitated rapid post-glacial recolonization. Overall, our findings highlight the roles of isolation by distance, Pleistocene climatic dynamics, geographic barriers, and sex-specific traits in shaping diversification in a highly mobile Neotropical bird.

The literature has identified poor nutrition as the leading factor in the manifestation of many behavioural issues in animals, including aggression, hyperalertness, and stereotypies. Literature focused on all species of interest consistently reported that although there were no significant differences in the richness of specific bacterial taxa in the microbiota of individual subjects with abnormal behaviour (termed alpha diversity), there was variability in species diversity between these subjects compared to controls (termed beta diversity). As seen in humans with mental disorders, animals exhibiting abnormal behaviour often have an enrichment of pro-inflammatory and lactic acid-producing bacteria and a reduction in butyrate-producing bacteria. It is evident from the literature that an association exists between gut microbiota diversity (and by extension, the concurrent production of microbial metabolites) and abnormal behavioural phenotypes across various species, including pigs, dogs, and horses. Similar microbiota population changes are also evident in human mental health patients. However, there are insufficient data to identify this association as a cause or effect. This review provides testable hypotheses for future research to establish causal relationships between gut microbiota and behavioural issues in animals, offering promising potential for the development of novel therapeutic and/or preventative interventions aimed at restoring a healthy gut-brain-immune axis to mitigate behavioural issues and, in turn, improve health, performance, and production in animals.

The color of the seed coat of common bean (Phaseolus vulgaris L.) is an important trait influencing marketability and consumer preferences. An understanding of the genetic mechanisms underlying seed coat color variation can aid in breeding programs aimed at improving esthetic and agronomic traits. This study investigates the genetic diversity and molecular mechanisms associated with seed coat color change in composite bean populations through phenotypic analysis and whole genome sequencing (WGS). Four composite populations and two standard varieties of common bean were cultivated over a two-year period and seed coat color and morphological traits were assessed. WGS was performed on 19 phenotypes and yielded 427 GB of data with an average sequencing depth of 30×. More than 8.6 million high-confidence single nucleotide polymorphisms (SNPs) were identified. Genetic diversity metrics such as nucleotide diversity (π), observed heterozygosity (Ho), expected heterozygosity (He) and allelic richness (Ar) were calculated. Population structure was analyzed using Fst, principal component analysis (PCA) and clustering. Cross-population statistics (XP-CLR and XP-EHH) were used to identify selection signals associated with seed coat color change. Gene Ontology (GO) and KEGG enrichment analyzes were performed for candidate genomic regions. Phenotypic analysis revealed significant differences in seed coat color among the four composite populations, with notable changes among years. The populations exhibited different growth habits and plant types, especially KIS_Amand and SRGB_00366, which showed the highest phenotypic diversity in seed coat color. WGS identified 8.6 million SNPs, with chromosomes 4 and 1 having the highest SNP density (11% each), while chromosomes 3 and 6 had the lowest. KIS_Amand had the highest genetic diversity (π = 0.222, Ar = 1.380) and SRGB_00189 the lowest (π = 0.067, Ar = 1.327). SRGB_00366 showed moderate genetic diversity (π = 0.173, Ar = 1.338) and INCBN_03048 showed medium diversity (π = 0.124, Ar = 1.047). The Fst values indicated a strong genetic differentiation, especially between the two standard varieties ETNA and Golden_Gate (Fst = 0.704) and the composite populations. Selective sweep analysis with XP-CLR and XP-EHH identified 118 significant regions associated with seed coat color change, with most regions located on chromosomes 4, 9, 10 and 11. Phosphatidylinositol signaling pathways were highly enriched in candidate regions, indicating that cellular transport mechanisms play a critical role in seed coat pigmentation. Key GO terms included phosphatidylinositol-biphosphate binding, exocytosis, and vesicle-mediated transport, suggesting a link between cellular transport and pigment deposition in the seed coat. The study demonstrates significant genetic diversity within and among common bean composite populations, with KIS_Amand and SRGB_00366 exhibiting the highest phenotypic and genetic variability. The identification of selective sweeps and the enrichment of phosphatidylinositol-related pathways provide new insights into the molecular mechanisms controlling seed coat color variation. The strong genetic differentiation between standard varieties and composite populations highlights the role of selective breeding in shaping the genetic landscape of common bean. The results suggest that variation in seed coat color is controlled by both regulatory and structural genetic changes, providing valuable information for breeding programs. This study provides a detailed analysis of the genetic architecture of seed coat color variation in common bean. The identification of key genomic regions and pathways associated with seed pigmentation improves our understanding of the complex genetic interactions underlying this trait. These results provide valuable genomic resources for future breeding efforts aimed at improving seed color and other important traits in common bean.

Selection-driven tumor evolution with public goods leads to patterns of clonal expansion consistent with neutral growth.