Karyotype analysis and sex determination in Australian Brush-turkeys (Alectura lathami)

Sexual differentiation across taxa may be due to genetic sex determination (GSD) and/or temperature sex determination (TSD). In many mammals, males are heterogametic (XY); whereas females are homogametic (XX). In most birds, the opposite is the case with females being heterogametic (ZW) and males the homogametic sex (ZZ). Many reptile spe- cies lack sex chromosomes, and instead, sexual differentiation is influenced by temperature with specific temperatures promoting males or females varying across species possessing this form of sexual differentiation, although TSD has recently been shown to override GSD in Australian central beaded dragons (Pogona vitticeps). There has been speculation that Australian Brush-turkeys (Alectura lathami) exhibit TSD alone and/or in combination with GSD. Thus, we sought to determine if this species possesses sex chromosomes. Blood was collected from one sexually mature female and two sexually mature males residing at Sylvan Heights Bird Park (SHBP) and shipped for karyotype analysis. Karyotype analysis revealed that contrary to speculation, Australian Brush-turkeys possess the classic avian ZW/ZZ sex chromosomes. It remains a possibility that a biased primary sex ratio of Austra- lian Brush-turkeys might be influenced by maternal condition prior to ovulation that result in her laying predominantly Z- or W-bearing eggs and/or sex-biased mortality due to higher sensitivity of one sex in environmental conditions. A better understanding of how maternal and extrinsic factors might differentially modulate ovulation of Z- or W-bearing eggs and hatching of developing chicks possessing ZW or ZZ sex chromosomes could be essential in conservation strategies used to save endangered members of Megapodiidae

Conservation and Immunogenomics of the Endangered White-winged Duck

White-winged Wood Ducks (WWD) are an endangered species native to southeast Asia. Efforts to conserve the species via captive breeding have been hindered because captive populations appear to be highly susceptible to avian tuberculosis (avian TB). This infection results in the premature mortality of over 80% of these birds. Therefore, despite the fact that birds can be readily bred in captivity, long-term maintenance is not yet possible. The underlying basis of this susceptibility is unknown. Thus, in my research I seek to understand the causes of this high disease susceptibility. Doing so will allow the development of strategies to reduce infection rates and facilitate conservation efforts aimed at maintaining this iconic species. In Chapter 1, I provide a review of captive WWD biology, specifically the management of the North American captive population, to serve as an important resource for future husbandry protocols aimed at improving the lifespan and reproductive success of WWD. I also identify priorities for the future of WWD in captivity. Due to their precipitous decline in captivity due to avian TB, in Chapter 2 I aim to characterize the effects of inbreeding in captivity relative to a wild population, and in particular, describe variation in immune-relevant portions of the genome. Finally, in Chapter 3, I characterize the microbiome of two pond types at Sylvan Heights Bird Park (SHBP). This comparison between natural bottom ponds and cement bottom ponds will help guide future management decisions of WWD in relation to mitigating exposure to the organism responsible for avian TB, Mycobacterium avium subsp. avium

Karyotype analysis and sex determination in Australian Brush-turkeys (Alectura lathami)

Sexual differentiation across taxa may be due to genetic sex determination (GSD) and/or temperature sex determination (TSD). In many mammals, males are heterogametic (XY); whereas females are homogametic (XX). In most birds, the opposite is the case with females being heterogametic (ZW) and males the homogametic sex (ZZ). Many reptile spe- cies lack sex chromosomes, and instead, sexual differentiation is influenced by temperature with specific temperatures promoting males or females varying across species possessing this form of sexual differentiation, although TSD has recently been shown to override GSD in Australian central beaded dragons (Pogona vitticeps). There has been speculation that Australian Brush-turkeys (Alectura lathami) exhibit TSD alone and/or in combination with GSD. Thus, we sought to determine if this species possesses sex chromosomes. Blood was collected from one sexually mature female and two sexually mature males residing at Sylvan Heights Bird Park (SHBP) and shipped for karyotype analysis. Karyotype analysis revealed that contrary to speculation, Australian Brush-turkeys possess the classic avian ZW/ZZ sex chromosomes. It remains a possibility that a biased primary sex ratio of Austra- lian Brush-turkeys might be influenced by maternal condition prior to ovulation that result in her laying predominantly Z- or W-bearing eggs and/or sex-biased mortality due to higher sensitivity of one sex in environmental conditions. A better understanding of how maternal and extrinsic factors might differentially modulate ovulation of Z- or W-bearing eggs and hatching of developing chicks possessing ZW or ZZ sex chromosomes could be essential in conservation strategies used to save endangered members of Megapodiidae

Comparative transcriptome analysis of Indian domestic duck reveals candidate genes associated with egg production

Egg production is an important economic trait and a key indicator of reproductive performance in ducks. Egg production is regulated by several factors including genes. However the genes involved in egg production in duck remain unclear. In this study, we compared the ovarian transcriptome of high egg laying (HEL) and low egg laying (LEL) ducks using RNA-Seq to identify the genes involved in egg production. The HEL ducks laid on average 433 eggs while the LEL ducks laid 221 eggs over 93 weeks. A total of 489 genes were found to be significantly differentially expressed out of which 310 and 179 genes were up and downregulated, respectively, in the HEL group. Thirty-eight differentially expressed genes (DEGs), including LHX9, GRIA1, DBH, SYCP2L, HSD17B2, PAR6, CAPRIN2, STC2, and RAB27B were found to be potentially related to egg production and folliculogenesis. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis suggested that DEGs were enriched for functions related to glutamate receptor activity, serine-type endopeptidase activity, immune function, progesterone mediated oocyte maturation and MAPK signaling. Protein–protein interaction network analysis (PPI) showed strong interaction between 32 DEGs in two distinct clusters. Together, these findings suggest a mix of genetic and immunological factors affect egg production, and highlights candidate genes and pathways, that provides an understanding of the molecular mechanisms regulating egg production in ducks and in birds more broadly

Karyotype results for Australian Brush-turkeys.

<p>G-band karyotype images without microchromosomes of A) female <i>A</i>. <i>lathami</i> demonstrating heterogametic ZW sex chromosomes and B) male <i>A</i>. <i>lathami</i> demonstrating homogametic ZZ sex chromosomes, C) G-band sex chromosomes of one female and two male <i>A</i>. <i>lathami</i>, and D) a C-band female metaphase image demonstrating weak to absent C-banding on the Z chromosome and complete C-banding on the W chromosome. For A and B, the numbers of corresponding chromosomes from the <i>G</i>. <i>gallus domesticus</i> karyotype are provided parenthetically.</p

Karyotype results for Australian Brush-turkeys.

<p>G-band karyotype images without microchromosomes of A) female <i>A</i>. <i>lathami</i> demonstrating heterogametic ZW sex chromosomes and B) male <i>A</i>. <i>lathami</i> demonstrating homogametic ZZ sex chromosomes, C) G-band sex chromosomes of one female and two male <i>A</i>. <i>lathami</i>, and D) a C-band female metaphase image demonstrating weak to absent C-banding on the Z chromosome and complete C-banding on the W chromosome. For A and B, the numbers of corresponding chromosomes from the <i>G</i>. <i>gallus domesticus</i> karyotype are provided parenthetically.</p

Dense sampling of bird diversity increases power of comparative genomics

Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity(1-4). Sparse taxon sampling has previously been proposed to confound phylogenetic inference(5), and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species. A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.Peer reviewe

Outcomes among trauma patients with duodenal leak following primary versus complex repair of duodenal injuries: An Eastern Association for the Surgery of Trauma multicenter trial

BACKGROUND: Duodenal leak is a feared complication of repair, and innovative complex repairs with adjunctive measures (CRAM) were developed to decrease both leak occurrence and severity when leaks occur. Data on the association of CRAM and duodenal leak are sparse, and its impact on duodenal leak outcomes is nonexistent. We hypothesized that primary repair alone (PRA) would be associated with decreased duodenal leak rates; however, CRAM would be associated with improved recovery and outcomes when leaks do occur. METHODS: A retrospective, multicenter analysis from 35 Level 1 trauma centers included patients older than 14 years with operative, traumatic duodenal injuries (January 2010 to December 2020). The study sample compared duodenal operative repair strategy: PRA versus CRAM (any repair plus pyloric exclusion, gastrojejunostomy, triple tube drainage, duodenectomy). RESULTS: The sample (N = 861) was primarily young (33 years) men (84%) with penetrating injuries (77%); 523 underwent PRA and 338 underwent CRAM. Complex repairs with adjunctive measures were more critically injured than PRA and had higher leak rates (CRAM 21% vs. PRA 8%, p \u3c 0.001). Adverse outcomes were more common after CRAM with more interventional radiology drains, prolonged nothing by mouth and length of stay, greater mortality, and more readmissions than PRA (all p \u3c 0.05). Importantly, CRAM had no positive impact on leak recovery; there was no difference in number of operations, drain duration, nothing by mouth duration, need for interventional radiology drainage, hospital length of stay, or mortality between PRA leak versus CRAM leak patients (all p \u3e 0.05). Furthermore, CRAM leaks had longer antibiotic duration, more gastrointestinal complications, and longer duration until leak resolution (all p \u3c 0.05). Primary repair alone was associated with 60% lower odds of leak, whereas injury grades II to IV, damage control, and body mass index had higher odds of leak (all p \u3c 0.05). There were no leaks among patients with grades IV and V injuries repaired by PRA. CONCLUSION: Complex repairs with adjunctive measures did not prevent duodenal leaks and, moreover, did not reduce adverse sequelae when leaks did occur. Our results suggest that CRAM is not a protective operative duodenal repair strategy, and PRA should be pursued for all injury grades when feasible. LEVEL OF EVIDENCE: Therapeutic/Care Management; Level IV