Ancient and Recent Hybridization in the Oreochromis Cichlid Fishes.

Cichlid fishes of the genus Oreochromis (tilapia) are among the most important fish for inland capture fisheries and global aquaculture. Deliberate introductions of non-native species for fisheries improvement and accidental escapees from farms have resulted in admixture with indigenous species. Such hybridization may be detrimental to native biodiversity, potentially leading to genomic homogenization of populations and the loss of important genetic material associated with local adaptation. By contrast, introgression may fuel diversification when combined with ecological opportunity, by supplying novel genetic combinations. To date, the role of introgression in the evolutionary history of tilapia has not been explored. Here we studied both ancient and recent hybridization in tilapia, using whole genome resequencing of 575 individuals from 23 species. We focused on Tanzania, a natural hotspot of tilapia diversity, and a country where hybridization between exotic and native species in the natural environment has been previously reported. We reconstruct the first genome-scale phylogeny of the genus and reveal prevalent ancient gene flow across the Oreochromis phylogeny. This has likely resulted in the hybrid speciation of one species, O. chungruruensis. We identify multiple cases of recent hybridization between native and introduced species in the wild, linked to the use of non-native species in both capture fisheries improvement and aquaculture. This has potential implications for both conservation of wild populations and the development of the global tilapia aquaculture industry.

Lateral line system diversification during the early stages of ecological speciation in cichlid fish.

BACKGROUND: The mechanosensory lateral line system is an important sensory modality in fishes, informing multiple behaviours related to survival including finding food and navigating in dark environments. Given its ecological importance, we may expect lateral line morphology to be under disruptive selection early in the ecological speciation process. Here we quantify the lateral line system morphology of two ecomorphs of the cichlid fish Astatotilapia calliptera in crater Lake Masoko that have diverged from common ancestry within the past 1,000 years. RESULTS: Based on geometric morphometric analyses of CT scans, we show that the zooplanktivorous benthic ecomorph that dominates the deeper waters of the lake has large cranial lateral line canal pores, relative to those of the nearshore invertebrate-feeding littoral ecomorph found in the shallower waters. In contrast, fluorescence imaging revealed no evidence for divergence between ecomorphs in the number of either superficial or canal neuromasts. We illustrate the magnitude of the variation we observe in Lake Masoko A. calliptera in the context of the neighbouring Lake Malawi mega-radiation that comprises over 700 species. CONCLUSIONS: These results provide the first evidence of divergence in this often-overlooked sensory modality in the early stages of ecological speciation, suggesting that it may have a role in the broader adaptive radiation process.

Sympatry and parapatry among rocky reef cichlids of Lake Victoria explained by female mating preferences.

Work on the Lake Victoria cichlids Pundamilia nyererei (red dorsum males, deeper water), Pundamilia pundamilia (blue males, shallower water) and related species pairs has provided insights into processes of speciation. Here, we investigate the female mating behaviour of 5 Pundamilia species and 4 of their F1 hybrids through mate choice trials and paternity testing. Complete assortative mating was observed among all sympatric species. Parapatric species with similar depth habitat distributions interbred whereas other parapatric and allopatric species showed complete assortative mating. F1 hybrids mated exclusively with species accepted by females of the parental species. The existence of complete assortative mating among some currently allopatric species suggests that pre-existing mating barriers could be sufficient to explain current patterns of co-existence, although, of course, many other factors may be involved. Regardless of the mechanism, mating preferences may influence species distribution in potentially hybridizing taxa, such as in the adaptive radiation of cichlid fish. We suggest that this at least partly explains why some species fail to establish breeding populations in locations where they are occasionally recorded. Our results support the notion that the mating preferences of potentially cross-breeding species ought to be included in coexistence theory.

Nuclear environmental DNA resolves fine-scale population genetic structure in an aquatic habitat.

There is considerable potential for nuclear genomic material in environmental DNA (eDNA) to inform us of population genetic structure within aquatic species. We tested if nuclear allelic composition data sourced from eDNA can resolve fine scale spatial genetic structure of the cichlid fish Astatotilapia calliptera in Lake Masoko, Tanzania. In this ∼35 m deep crater lake the species is diverging into two genetically distinguishable ecomorphs, separated by a thermo-oxycline at ∼15 m that divides biologically distinct water masses. We quantified population genetic structure along a depth transect using single nucleotide polymorphisms (SNPs) derived from genome sequencing of 530 individuals. This population genetic structure was reflected in a focal set of SNPs that were also reliably amplified from eDNA - with allele frequencies derived from eDNA reflecting those of fish within each depth zone. Thus, by targeting known genetic variation between populations within aquatic eDNA, we measured genetic structure within the focal species.

A new species of Lethrinops (Cichliformes: Cichlidae) from a Lake Malawi satellite lake, believed to be extinct in the wild.

A new species of cichlid fish, Lethrinops chilingali is described from specimens collected from Lake Chilingali, near Nkhotakota, Malawi. It is assigned to the genus Lethrinops based on the form of the lower jaw dental arcade and by the absence of traits diagnostic of the phenotypically similar Ctenopharynx, Taeniolethrinops and Tramitichromis. It also lacks the enlarged cephalic lateral line canal pores found in species of Alticorpus and Aulonocara. The presence of a broken horizontal stripe on the flanks of females and immature/non-territorial males of Lethrinops chilingali distinguishes them from all congeners, including Lethrinops lethrinus, in which the stripe is typically continuous. Lethrinops chilingali also has a relatively shorter snout, shorter lachrymal bone and less ventrally positioned mouth than Lethrinops lethrinus. It appears likely that Lethrinops chilingali is now extinct in the wild, as this narrow endemic species has not been positively recorded in the natural environment since 2009. Breeding populations remain in captivity.

Ecological Speciation Promoted by Divergent Regulation of Functional Genes Within African Cichlid Fishes.

Rapid ecological speciation along depth gradients has taken place repeatedly in freshwater fishes, yet molecular mechanisms facilitating such diversification are typically unclear. In Lake Masoko, an African crater lake, the cichlid Astatotilapia calliptera has diverged into shallow-littoral and deep-benthic ecomorphs with strikingly different jaw structures within the last 1,000 years. Using genome-wide transcriptome data, we explore two major regulatory transcriptional mechanisms, expression and splicing-QTL variants, and examine their contributions to differential gene expression underpinning functional phenotypes. We identified 7,550 genes with significant differential expression between ecomorphs, of which 5.4% were regulated by cis-regulatory expression QTLs, and 9.2% were regulated by cis-regulatory splicing QTLs. We also found strong signals of divergent selection on differentially expressed genes associated with craniofacial development. These results suggest that large-scale transcriptome modification plays an important role during early-stage speciation. We conclude that regulatory variants are important targets of selection driving ecologically relevant divergence in gene expression during adaptive diversification.

Epigenetic divergence during early stages of speciation in an African crater lake cichlid fish.

Epigenetic variation can alter transcription and promote phenotypic divergence between populations facing different environmental challenges. Here, we assess the epigenetic basis of diversification during the early stages of speciation. Specifically, we focus on the extent and functional relevance of DNA methylome divergence in the very young radiation of Astatotilapia calliptera in crater Lake Masoko, southern Tanzania. Our study focuses on two lake ecomorphs that diverged approximately 1,000 years ago and a population in the nearby river from which they separated approximately 10,000 years ago. The two lake ecomorphs show no fixed genetic differentiation, yet are characterized by different morphologies, depth preferences and diets. We report extensive genome-wide methylome divergence between the two lake ecomorphs, and between the lake and river populations, linked to key biological processes and associated with altered transcriptional activity of ecologically relevant genes. Such genes differing between lake ecomorphs include those involved in steroid metabolism, hemoglobin composition and erythropoiesis, consistent with their divergent habitat occupancy. Using a common-garden experiment, we found that global methylation profiles are often rapidly remodeled across generations but ecomorph-specific differences can be inherited. Collectively, our study suggests an epigenetic contribution to the early stages of vertebrate speciation.

A new species of deep-water Lethrinops (Cichlidae) from Lake Malawi.

A new species of cichlid fish, Lethrinops atrilabris is described from specimens collected by trawling at a depth of around 90 m off Monkey Bay, southern Lake Malawi. It is assigned to the genus Lethrinops on the basis of its vertical flank barring, lack of enlarged cephalic lateral line canal pores and the form of the lower jaw dental arcade. It can be distinguished from congeneric species by its male breeding dress of contrasting flank barring and dark ventral surface, most strikingly on the lips, throat and chest, its relatively small known maximum size [<75 mm standard length (SL)], large eyes (38%-41% head length), laterally compressed body (depth 2.5-2.7 times max head width) and lower gill raker count (13-14).

Oca2 targeting using CRISPR/Cas9 in the Malawi cichlid Astatotilapia calliptera.

Identifying genetic loci underlying trait variation provides insights into the mechanisms of diversification, but demonstrating causality and characterizing the role of genetic loci requires testing candidate gene function, often in non-model species. Here we establish CRISPR/Cas9 editing in Astatotilapia calliptera, a generalist cichlid of the remarkably diverse Lake Malawi radiation. By targeting the gene oca2 required for melanin synthesis in other vertebrate species, we show efficient editing and germline transmission. Gene edits include indels in the coding region, probably a result of non-homologous end joining, and a large deletion in the 3' untranslated region due to homology-directed repair. We find that oca2 knock-out A. calliptera lack melanin, which may be useful for developmental imaging in embryos and studying colour pattern formation in adults. As A. calliptera resembles the presumed generalist ancestor of the Lake Malawi cichlids radiation, establishing genome editing in this species will facilitate investigating speciation, adaptation and trait diversification in this textbook radiation.

Early Pars Plana Vitrectomy in Acute Endophthalmitis: The Manchester Series.

BACKGROUND AND OBJECTIVE: Current literature lacks good-quality evidence regarding the outcomes of early pars plana vitrectomy (PPV) for acute exogenous endophthalmitis. The aim for this study was to analyze and discuss the outcomes of PPV for endophthalmitis in a UK tertiary hospital. PATIENTS AND METHODS: This study was a retrospective case series. The clinical records of consecutive patients who had PPV for acute exogenous endophthalmitis were reviewed. Demographic data, etiology, timing of onset, timing of PPV, intraand postoperative complications, baseline and final best-corrected visual acuity (BCVA), therapeutic regimens, and microbiology details were collected. Primary efficacy and safety outcome measures were BCVA improvement of two or more logMAR lines and intra- or postoperative complications, respectively. RESULTS: Forty-one patients with a median age of 76 (interquartile range, 64 to 82) years were studied. The most common etiology was intravitreal injection (41%), followed by phacoemulsification (34%). Median interval to PPV was 1.0 (interquartile range, 1.0 to 3.0) days. In a multivariate model controlling for age, baseline BCVA, microbiology positivity, and etiology (post-intravitreal injection), PPV after 24 hours was seven times more likely to achieve significant BCVA improvement (odds ratio, 7.47; 95% confidence interval, 1.12 to 49.66; P = .038). PPV within 24 hours of presentation was associated with more intraoperative complications. CONCLUSIONS: Favorable outcomes may be achieved with current antibiotic regimens and PPV for endophthalmitis. The series suggests that an early surgical intervention may be associated with poorer functional outcomes. Tap and inject at presentation, followed by a semi-urgent PPV as required, seems to be a sensible approach. [Ophthalmic Surg Lasers Imaging Retina. 2022;53:96-102.].

Whole genome resequencing data enables a targeted SNP panel for conservation and aquaculture of Oreochromis cichlid fishes.

Cichlid fish of the genus Oreochromis form the basis of the global tilapia aquaculture and fisheries industries. Broodstocks for aquaculture are often collected from wild populations, which in Africa may be from locations containing multiple Oreochromis species. However, many species are difficult to distinguish morphologically, hampering efforts to maintain good quality farmed strains. Additionally, non-native farmed tilapia populations are known to be widely distributed across Africa and to hybridize with native Oreochromis species, which themselves are important for capture fisheries. The morphological identification of these hybrids is particularly unreliable. Here, we describe the development of a single nucleotide polymorphism (SNP) genotyping panel from whole-genome resequencing data that enables targeted species identification in Tanzania. We demonstrate that an optimized panel of 96 genome-wide SNPs based on FST outliers performs comparably to whole genome resequencing in distinguishing species and identifying hybrids. We also show this panel outperforms microsatellite-based and phenotype-based classification methods. Case studies indicate several locations where introduced aquaculture species have become established in the wild, threatening native Oreochromis species. The novel SNP markers identified here represent an important resource for assessing broodstock purity in hatcheries and helping to conserve unique endemic biodiversity.

STEP-WISE APPROACH TO THE MANAGEMENT OF SUBMACULAR HEMORRHAGE USING PNEUMATIC DISPLACEMENT AND VITRECTOMY: The Manchester Protocol.

PURPOSE: To evaluate a sequential approach of pneumatic displacement followed by vitrectomy (pars plana vitrectomy) in failed cases to deal with submacular hemorrhage (SMH) of various etiologies. METHODS: Retrospective, nonrandomized interventional case series of consecutive patients with SMH of up to 2 weeks' duration, who were treated with a stepwise approach. Step 1 involved intravitreal injection of 0.3 mL 100% C3F8 and recombinant tissue plasminogen activator 50 µg/0.1 mL. If unsuccessful, a prompt pars plana vitrectomy with subretinal recombinant tissue plasminogen activator 50 µg/0.1 mL and 20% SF6 gas tamponade was performed as a second attempt to displace the SMH. RESULTS: Thirty-one patients with SMH underwent pneumatic displacement; 24 (77.4%) had a successful outcome without further intervention. The mean presenting visual acuity of the "successful cohort" was 1.34 logMAR (20/440 Snellen), improving to 0.83 logMAR (20/135 Snellen) 1 month after treatment. Five of the seven patients with failed pneumatic displacement underwent pars plana vitrectomy with subretinal recombinant tissue plasminogen activator at an average of 5 days poststep 1, with successful SMH displacement in 3 patients, giving an overall success of 87.1% for this treatment protocol. CONCLUSION: A sequential approach of expansile gas injection followed by prompt pars plana vitrectomy, aided by recombinant tissue plasminogen activator at both steps, is a coherent, logical pathway to treat SMH with high anatomical and functional success.

Mapping epigenetic divergence in the massive radiation of Lake Malawi cichlid fishes.

Epigenetic variation modulates gene expression and can be heritable. However, knowledge of the contribution of epigenetic divergence to adaptive diversification in nature remains limited. The massive evolutionary radiation of Lake Malawi cichlid fishes displaying extensive phenotypic diversity despite extremely low sequence divergence is an excellent system to study the epigenomic contribution to adaptation. Here, we present a comparative genome-wide methylome and transcriptome study, focussing on liver and muscle tissues in phenotypically divergent cichlid species. In both tissues we find substantial methylome divergence among species. Differentially methylated regions (DMR), enriched in evolutionary young transposons, are associated with transcription changes of ecologically-relevant genes related to energy expenditure and lipid metabolism, pointing to a link between dietary ecology and methylome divergence. Unexpectedly, half of all species-specific DMRs are shared across tissues and are enriched in developmental genes, likely reflecting distinct epigenetic developmental programmes. Our study reveals substantial methylome divergence in closely-related cichlid fishes and represents a resource to study the role of epigenetics in species diversification.

Rare morph Lake Malawi mbuna cichlids benefit from reduced aggression from con- and hetero-specifics.

Balancing selection is important for the maintenance of polymorphism as it can prevent either fixation of one morph through directional selection or genetic drift, or speciation by disruptive selection. Polychromatism, the presence of multiple genetically determined colour phenotypes, can be maintained if the fitness of alternative morphs depends on the relative frequency in a population. In aggressive species, negative frequency-dependent antagonism can prevent an increase in the frequency of rare morphs as they would only benefit from increased fitness while they are rare. Heterospecific aggression is common in nature and has the potential to contribute to rare morph advantage. Here we carry out field observations and laboratory aggression experiments with mbuna cichlids from Lake Malawi, to investigate the role of con- and heterospecific aggression in the maintenance of polychromatism and identify benefits to rare morphs which are likely to result from reduced aggression. We hypothesize that rare morph individuals receive less aggression than common morph individuals and therefore have an ecological advantage. Within species we found that males and females bias aggression towards their own morph, adding to the evidence that inherent own-morph aggression biases can contribute to balancing selection. Over-representation of rare morph territory owners may be influenced by two factors; higher tolerance of different morph individuals as neighbours, and the ability of rare morphs to spend more time feeding. Reduced aggression to rare morph individuals by heterospecifics may also contribute to rare morph advantage.

Towards complete and error-free genome assemblies of all vertebrate species.

High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species1-4. To address this issue, the international Genome 10K (G10K) consortium5,6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling highly accurate and nearly complete reference genomes. Here we present lessons learned from generating assemblies for 16 species that represent six major vertebrate lineages. We confirm that long-read sequencing technologies are essential for maximizing genome quality, and that unresolved complex repeats and haplotype heterozygosity are major sources of assembly error when not handled correctly. Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries. These include the identification of many false gene duplications, increases in gene sizes, chromosome rearrangements that are specific to lineages, a repeated independent chromosome breakpoint in bat genomes, and a canonical GC-rich pattern in protein-coding genes and their regulatory regions. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences.

Outcomes of suprachoroidal haemorrhage drainage with and without vitrectomy: a 10-year study.

PURPOSE: The management of suprachoroidal haemorrhage (SCH) remains a challenge. We aimed to analyse and discuss the safety and efficacy outcomes of SCH drainage surgery over a 10-year period in one of the largest tertiary centres in the UK. METHODS: Retrospective observational study of consecutive patients who underwent SCH drainage in Manchester Royal Eye Hospital over a 10-year period (from 2008 to 2018). Safety and efficacy were assessed by analysing surgery-related complications and functional and anatomical success. Outcomes of those who underwent external drainage alone versus combined drainage and vitrectomy were compared. RESULTS: Twenty consecutive patients with a mean age of 70 ± 19 years were studied. Age over 70 years, hypertension, cardiovascular disease, and glaucoma were the most common risk factors for SCH. Eleven patients underwent external drainage alone and nine patients had combined vitrectomy and drainage. Overall, mean pre-operative BCVA improved from 2.22 ± 0.26 logMAR (20/3319 Snellen) to 1.42 ± 1.02 LogMAR (20/526 Snellen) at last follow-up visit (p = 0.002). Severe hypotony occurred in 4 patients. Overall anatomical and functional success rates were both 75%. CONCLUSIONS: Drainage of SCH with or without vitrectomy is a valuable approach in the management of extensive SCH, a condition generally associated with poor prognosis.

Newly discovered cichlid fish biodiversity threatened by hybridization with non-native species.

Invasive freshwater fishes are known to readily hybridize with indigenous congeneric species, driving loss of unique and irreplaceable genetic resources. Here we reveal that newly discovered (2013-2016) evolutionarily significant populations of Korogwe tilapia (Oreochromis korogwe) from southern Tanzania are threatened by hybridization with the larger invasive Nile tilapia (Oreochromis niloticus). We use a combination of morphology, microsatellite allele frequencies and whole genome sequences to show that O. korogwe from southern lakes (Nambawala, Rutamba and Mitupa) are distinct from geographically disjunct populations in northern Tanzania (Zigi River and Mlingano Dam). We also provide genetic evidence of O. korogwe × niloticus hybrids in three southern lakes and demonstrate heterogeneity in the extent of admixture across the genome. Finally, using the least admixed genomic regions we estimate that the northern and southern O. korogwe populations most plausibly diverged ~140,000 years ago, suggesting that the geographical separation of the northern and southern groups is not a result of a recent translocation, and instead these populations represent independent evolutionarily significant units. We conclude that these newly discovered and phenotypically unique cichlid populations are already threatened by hybridization with an invasive species, and propose that these irreplaceable genetic resources would benefit from conservation interventions.

A Psychotherapy Private Practice Social Work Practicum: Expanding Our Boundaries of Field Education Placement.

Many social workers go into private practice, providing crucial mental health services; however, there is a dearth in the scholarship outlining the social work student training for these career options. It may be argued that social work students receive little or no clinical training on how to run a private practice providing psychotherapy services. To mend this pedagogical shortcoming, a private practice field education placement is a legitimate teaching opportunity to prepare social work students to meet the mental health needs of individuals, families, and the public. Authors drew on borderlands theory described by Gloria Anzaldua as a contested space that focuses on "both and" thinking, which resonated with a sense of navigating a border filled with cultural tension between private practice and social work. Five social workers explore their unique experiences of a private practice field education placement using borderlands theory as a lens. Qualitative analysis of autoethnography narratives resulted in six themes: (1) benefits to private practice site, (2) preparation for social work, (3) private practice is social work, (4) balanced picture, (5) practicum landscape, and (6) learning opportunities. The article concludes with recommendations for social work education and research.

Ancestral Hybridization Facilitated Species Diversification in the Lake Malawi Cichlid Fish Adaptive Radiation.

The adaptive radiation of cichlid fishes in East African Lake Malawi encompasses over 500 species that are believed to have evolved within the last 800,000 years from a common founder population. It has been proposed that hybridization between ancestral lineages can provide the genetic raw material to fuel such exceptionally high diversification rates, and evidence for this has recently been presented for the Lake Victoria region cichlid superflock. Here, we report that Lake Malawi cichlid genomes also show evidence of hybridization between two lineages that split 3-4 Ma, today represented by Lake Victoria cichlids and the riverine Astatotilapia sp. "ruaha blue." The two ancestries in Malawi cichlid genomes are present in large blocks of several kilobases, but there is little variation in this pattern between Malawi cichlid species, suggesting that the large-scale mosaic structure of the genomes was largely established prior to the radiation. Nevertheless, tens of thousands of polymorphic variants apparently derived from the hybridization are interspersed in the genomes. These loci show a striking excess of differentiation across ecological subgroups in the Lake Malawi cichlid assemblage, and parental alleles sort differentially into benthic and pelagic Malawi cichlid lineages, consistent with strong differential selection on these loci during species divergence. Furthermore, these loci are enriched for genes involved in immune response and vision, including opsin genes previously identified as important for speciation. Our results reinforce the role of ancestral hybridization in explosive diversification by demonstrating its significance in one of the largest recent vertebrate adaptive radiations.

Treatment decisions of UK hospital optometrists and ophthalmologists in patients with nAMD: a vignette study.

PURPOSE: A vignette study to examine treatment decisions made by UK hospital optometrists in patients with neovascular age-related macular degeneration (nAMD) and the effect of optometrists' experience on agreement. METHODS: Patients with nAMD attending Manchester Royal Eye Hospital, Manchester, UK were identified as potential candidates for the case series of vignettes. The cases were chosen to reflect a varied case-mix with respect to difficulty as well as ensuring good quality of the images. Each vignette included a history summary consisting of the number of previous injections given and visual acuity measurements at baseline, the previous visit, and the current visit. Images were compiled to show baseline fundus photographs and ocular coherence tomography (OCT) images with the current visit images on which the treatment decision was to be made along with the images from the previous visit. Hospital optometrists were recruited and asked to complete the series of vignettes, deciding if treatment was required at that visit and how confident they felt with that decision. Their responses were compared to the reference standard created by a consensus of consultant ophthalmologists with a sub-speciality interest in medical retina. RESULTS: Regarding treatment decision for optometrists, the percentage correct value was 75% with the sensitivity being 75.6% (95% CI 70.1-80.3) and the specificity as 75.1% (95% CI 72.1-77.8). No statistically significant difference was found between differing levels of experience. However, there was a significant difference in confidence levels between groups. Potentially sight threatening decisions accounted for 6.4% of the optometrists' decisions, 3.5% were made with a high confidence rating suggesting no discussion with an ophthalmologist was required. CONCLUSIONS: Although the optometrists showed modest agreement with the reference standard in a series of cases that have higher than average complexity, the optometrists showed a similar amount of variability within their treatment decisions compared to the reference standard. The optometrists were therefore not inferior in their performance compared to the ophthalmologists and this can be seen as supporting evidence for their extended role within this clinical area. Experience did not have an effect on 'correct' treatment decisions although there was a statistically significant effect on increasing confidence of treatment decision.