Runs of homozygosity and analysis of inbreeding depression

Pedigree information was traditionally used to assess inbreeding. The availability of high-density marker panels provides an alternative to assess inbreeding, particularly in the presence of incomplete and error-prone pedigrees. Assessment of autozygosity across chromosomal segments using runs of homozygosity (ROH) has emerged as a valuable tool to estimate inbreeding due to its general flexibility and ability to quantify the chromosomal contribution to genome-wide inbreeding. Unfortunately, the identification of ROH segments is sensitive to the parameters used during the search process. These parameters are heuristically set, leading to significant variation in the results. The minimum length required to identify an ROH segment has major effects on the estimation of inbreeding and inbreeding depression, yet it is arbitrarily set. To overcome this limitation, a search algorithm to approximate mutation enrichment was developed to determine the minimum length of ROH segments. It consists of finding genome segments with significant effect differences in trait means between animals with high and low burdens of autozygous intervals with a specific length. The minimum length could be determined heuristically as the smallest interval at which a significant signal is detected. The proposed method was tested in an inbred Hereford cattle population genotyped for 30,220 SNPs. Phenotypes recorded for six traits were used for the approximation of mutation loads. The estimated minimum length was around 1 Mb for yearling weight (YW) and average daily gain (ADG) and 4 Mb for birth weight and weaning weight. These trait-specific thresholds estimated using the proposed method could be attributed to a trait-dependent effect of homozygosity. The detection of significant inbreeding effects was well aligned with the estimated thresholds, especially for YW and ADG. Although highly deleterious alleles are expected to be more frequent in recent inbreeding (long ROH), short ROH segments (<5 Mb) could contain a large number of less deleterious mutations with substantial joint effects on some traits (YW and ADG). Our results highlight the importance of accurate estimation of the ROH-based inbreeding and the necessity to consider a trait-specific minimum length threshold for the identification of ROH segments in inbreeding depression analyses. These thresholds could be determined using the proposed method provided the availability of phenotypic information.     

Corrosion of metal fasteners embedded in acetylated and untreated wood at different moisture contents

ABSTRACT

Acetylated wood is now commercially available and designed to be used in certain outdoor applications as an alternative to preservative-treated wood. Fastener corrosion can be a concern in preservative treated wood when the wood remains wet for long periods. However, little data on the corrosiveness of acetylated wood exists beyond the product literature. Here we examine the corrosiveness of commercially obtained acetylated wood and compare it against unmodified (untreated) southern pine (Pinus spp.). Corrosion rates of plain carbon steel, hot dip galvanized steel, and stainless steel were calculated gravimetrically after a one year exposed in the wood. Four different moisture conditions were examined: 90% relative humidity (RH), 95% RH, 100% RH, and a fully water saturated condition. When compared to literature data on the corrosion of fasteners in preservative treated wood at 100% RH, the acetylated wood had much lower steel corrosion rates than all preservatives examined; the measured corrosion rates for galvanized steel were lower than all preservatives except chromated copper arsenate. These measured corrosion rates across a range of moisture conditions can be used to inform the selection of appropriate corrosion resistant fasteners when building with acetylated wood.     

Stifle joint osteoarthritis at the time of diagnosis of cranial cruciate ligament injury is higher in Boxers and in dogs weighing more than 35 kilograms

Osteoarthritis is a ubiquitous disease in dogs. The purpose of this retrospective study was to characterize the severity and distribution of osteoarthritis (OA) within the joint and to identify differences among dog breeds in the severity of OA in the cranial cruciate ligament (CCL)‐deficient stifle joint. Radiographs of 240 stifles from 51 Boxers, 66 German Shepherds, 100 Labrador Retrievers, and 23 Siberian Huskies with confirmed CCL rupture were included. Radiographs of the stifle joint were evaluated and OA severity was graded at 33 sites within and around the joint, and patella alta was graded as present or absent for a potential total stifle OA score of 100. Osteophyte size was correlated to OA severity score. Total OA scores were calculated and compared within and between breeds globally as well as at each joint site. Dogs weighing >35 kg had a higher total OA score than those weighing <35 kg. Osteoarthritis scores were highest at the apical patella, proximolateral tibia, and sesamoid bones, corresponding to the proximal, lateral, and caudal aspects of the joint, respectively. No statistically significant differences were found among the mean OA scores of various stifle joint regions. Boxer dogs had a higher total OA score than other breeds. We concluded that dogs have a consistent distribution pattern of OA within the stifle joint after CCL injury. Radiographic OA is more severe in the proximal, lateral, and caudal aspects of the joint. Boxers had more severe OA than the other breeds evaluated in the study.     

Assessing the suitability of a partial water reuse system for rearing juvenile Chinook salmon for stocking in Washington State

To assess the suitability of water reuse technology for raising Pacific salmon Oncorhynchus spp. for stocking purposes, fish health and welfare were compared between two groups of juvenile Chinook salmon O. tshawytscha from the same spawn: one group was reared in a pilot partial water reuse system (circular tanks), and the other group was reared in a flow-through raceway. This observational study was carried out over a 21-week period in Washington State. Reuse and raceway fish were sampled repeatedly for pathogen screening and histopathology; fin erosion and whole-blood characteristics were also evaluated. By the study's end, no listed pathogens were isolated from either cohort, and survival was 99.3% and 99.0% in the reuse and raceway groups, respectively. Condition factor was 1.28 in raceway fish and 1.14 in reuse fish; this difference may have been attributable to occasional differences in feeding rates between the cohorts. Fin indices (i.e., length of the longest dorsal or caudal fin ray, standardized by fork length) were lower in reuse fish than in raceway fish, but fin erosion was not grossly apparent in either cohort. The most consistent histological lesion was gill epithelial hypertrophy in reuse fish; however, blood analyses did not suggest any corresponding physiological imbalances. Overall, results suggest that water reuse technology can be employed in rearing juvenile anadromous salmonids for stocking purposes.     

Atypical and malignant canine intracranial meningiomas may have lower apparent diffusion coefficient values than benign tumors

Canine intracranial meningiomas can be graded based on histological classification as benign (grade I), atypical (grade II), and anaplastic or malignant (grade III). In people, grade II/III meningiomas behave more aggressively, have a higher potential for recurrence after surgical resection, and have lower apparent diffusion coefficient (ADC) values with diffusion weighted imaging (DWI). In this retrospective analytical cross‐sectional study, 42 dogs had ADC values quantified in an attempt to differentiate tumor histologic grade. Our hypothesis was that ADC values would be significantly lower in grade II and III versus grade I meningiomas in dogs. On each ADC image, a polygonal region of interest (ROI) was hand‐drawn along the lesion's periphery, excluding fluid‐filled and hemorrhagic regions. Mean ADC value (ADC_mean) and minimum ADC value (ADC_min) were calculated. Additionally, two smaller, ovoid ROI were drawn within the lesion with mean ADC calculated (ADC_{mean sR} and ADC_{min sR}). Normalized ADC values using white matter were also calculated (ADC_n and ADC_{n sR}). Grades of each tumor were assigned based on histopathology review. Association between ADC parameters and histological grade was tested by means of two‐sample t‐tests. There were 14 grade I (33.3%), 25 grade II (59.5%), and three grade III (7.2%) meningiomas. ADC_{mean sR} and ADC_{min sR} were significantly lower when comparing grade II/III to grade I (P < .05). Grade II tumors had significantly lower ADC_mean, ADC_{mean sR}, ADC_{min sR}, ADC_n, and ADC_{n sR} than grade I meningiomas. This preliminary study supports the potential of ADC values to help predict the histological grade of intracranial meningiomas in dogs.     

Prediction,structure characterization,and evolutionary analysis of Erwinia psidii putative type III effectors

Erwinia psidii is a gram-negative bacterium that threatens both guava and eucalypt plantations in several countries. Despite the economic importance of both crops, nothing is currently known about the molecular mechanisms underlying E. psidii pathogenicity and, consequently, how it evolved to infect Eucalyptus species besides its presumed native host Psidium guajava. In this study, we predicted putative type III secretion system effectors that may play important roles during plant–E. psidii interactions and conducted effector structure and phylogenetic analyses to gain important insights into their function and evolution. For that, the whole genomes of four E. psidii strains that exhibit differential aggressiveness towards eucalypt clones were sequenced and their effector repertoires predicted based on sequence identity with known effectors of the model phytopathogen Erwinia amylovora. Only proteins sharing significant sequence identity with the DspE and Eop1 effectors were found. Here, it is shown that these two E. psidii effectors retain all structural characteristics of their corresponding protein superfamilies, but exhibit allelic variations that are consistent with the observed aggressiveness differences between strains. Phylogenetic analyses revealed that whereas E. psidii housekeeping gene sequences are more closely related to those from Erwinia tracheiphila, the effector (either nucleotide or amino acid) sequences are more closely related to their Pantoea agglomerans counterparts, suggesting that dspE and eop1 were both acquired through horizontal gene transfer from the latter bacterial species. The results of this study provide important insights on E. psidii pathogenicity and set the stage for future effector functional studies.     

Markov models of land cover dynamics in a southern Great Plains grassland region

Grassland regions of the southern Great Plains are fragmented by agricultural activity and many habitat remnants have experienced encroachment by juniper (Juniperus virginiana L.). Recently, many cropland areas have been converted to monoculture grassland (pastures) and enrolled into the Conservation Reserve Program (CRP). Our objectives were to develop spatial and temporal Markov models to characterize land cover dynamics relative to juniper expansion and CRP using aerial photography from 1965, 1981, and 1995. We used landscapes surrounding three Breeding Bird Survey routes with varying levels of juniper encroachment in Oklahoma as study areas. As expected, land cover changes from 1965 to 1995 included increases in juniper woodland, mixed juniper-deciduous woodland, and pastures from CRP activity. Markov models revealed that juniper had a low likelihood of self-replacement in early stages of encroachment. In all areas, relatively little native grassland was lost to juniper encroachment, but other native habitat types such as deciduous woodland were heavily impacted. Transition probabilities for land cover dynamics varied significantly both spatially and temporally. Projections of these raw transition matrices produced widely varying models of future land cover conditions. By modifying the matrices to account for recent and potential socio-political and ecological changes occurring in this region, a number of more plausible land cover scenarios were produced than those resulting from simple projections of raw transition matrices.     

What is the ecological footprint of aquaculture after 5 decades of competition between mangrove conservation and shrimp farm development?

1. Among the several threats to the conservation of mangrove ecosystems in most South Asian countries, shrimp farming is predominant. Since the introduction of shrimp farming in Sri Lanka in the 1980s, mangroves on the island’s north-western coast have been continually cleared to create new shrimp farms, leading to a decline in the social-ecological services provided by the mangrove ecosystems.
2. Using aerial (1973) and satellite (1996–2020) images, this study assessed areal changes in mangroves and shrimp farms in the Pambala-Chilaw lagoon complex and Ihala Mahawewa, as well as the ecological footprint of shrimp farming in the study area.
3. Mangroves around the Chilaw lagoon had decreased in areal extent by 45% from 1973 to 2020 of which 92% of this change was attributed to shrimp farming. There was, however, a decrease in the areal extent of shrimp farms from 2001 to 2020, and a corresponding increase in mangroves from 2006 to 2020.
4. The ecological footprint of shrimp farming was assessed by comparing the expected surface ratios with those recorded for shrimp farms with mangroves and surface water bodies in the study area from 1973 to 2020. The results showed that the current shrimp farming was unsustainable (i.e. high ecological footprint).
5. While the results support the current view that there is cause for cautious optimism with mangrove conservation (as evidenced by an increase in mangrove areal extent), it also reveals that semi-intensive shrimp farming in Sri Lanka and probably other similar tropical countries is unsustainable.
6. If immediate actions such as effective regulation of shrimp farming activities and mangrove restoration are not taken, the mangrove ecosystem will continue to decline.