Reduction of genetic diversity in 'Alala (Hawaiian crow; Corvus hawaiiensis) between the late 1800s and the late 1900s.

Genetic and genomic data are increasingly used to aid conservation management of endangered species by providing insights into evolutionary histories, factors associated with extinction risks, and potential for future adaptation. For the 'Alala, or Hawaiian crow (Corvus hawaiiensis), genetic concerns include negative correlations between inbreeding and hatching success. However, it is unclear if low genetic diversity and inbreeding depression are consequences of a historical population bottleneck, or if 'Alala had historically low genetic diversity that predated human influence, perhaps as a result of earlier declines or founding events. In this study, we applied a hybridization-based sequence capture to generate a genome-wide single nucleotide polymorphism (SNP) dataset for comparing historical specimens collected in the 1890s, when 'Alala were more numerous, to samples taken between 1973 and 1998, when 'Alala population densities were near the lowest documented levels in the wild, prior to all individuals being collected for captive rearing. We found low genome-wide diversity in both sample groups, however, the modern sample group (1973 to 1998 cohort) exhibited relatively fewer polymorphic alleles, a lower proportion of polymorphic loci, and lower observed heterozygosity, consistent with a population decline and potential bottleneck effects. These results combined with a current low population size highlight the importance of continued efforts by conservation managers to mitigate inbreeding and maintain founder representation to preserve what genetic diversity remains.

The Transmission Patterns of the Endosymbiont Wolbachia within the Hawaiian Drosophilidae Adaptive Radiation.

The evolution of endosymbionts and their hosts can lead to highly dynamic interactions with varying fitness effects for both the endosymbiont and host species. Wolbachia, a ubiquitous endosymbiont of arthropods and nematodes, can have both beneficial and detrimental effects on host fitness. We documented the occurrence and patterns of transmission of Wolbachia within the Hawaiian Drosophilidae and examined the potential contributions of Wolbachia to the rapid diversification of their hosts. Screens for Wolbachia infections across a minimum of 140 species of Hawaiian Drosophila and Scaptomyza revealed species-level infections of 20.0%, and across all 399 samples, a general infection rate of 10.3%. Among the 44 Wolbachia strains we identified using a modified Wolbachia multi-locus strain typing scheme, 30 (68.18%) belonged to supergroup B, five (11.36%) belonged to supergroup A, and nine (20.45%) had alleles with conflicting supergroup assignments. Co-phylogenetic reconciliation analysis indicated that Wolbachia strain diversity within their endemic Hawaiian Drosophilidae hosts can be explained by vertical (e.g., co-speciation) and horizontal (e.g., host switch) modes of transmission. Results from stochastic character trait mapping suggest that horizontal transmission is associated with the preferred oviposition substrate of the host, but not the host's plant family or island of occurrence. For Hawaiian Drosophilid species of conservation concern, with 13 species listed as endangered and 1 listed as threatened, knowledge of Wolbachia strain types, infection status, and potential for superinfection could assist with conservation breeding programs designed to bolster population sizes, especially when wild populations are supplemented with laboratory-reared, translocated individuals. Future research aimed at improving the understanding of the mechanisms of Wolbachia transmission in nature, their impact on the host, and their role in host species formation may shed light on the influence of Wolbachia as an evolutionary driver, especially in Hawaiian ecosystems.

Genetic diversity, structure, and effective population size of an endangered, endemic hoary bat, 'ope'ape'a, across the Hawaiian Islands.

Island bat species are disproportionately at risk of extinction, and Hawai'i's only native terrestrial land mammal, the Hawaiian hoary bat (Lasiurus semotus) locally known as 'ope'ape'a, is no exception. To effectively manage this bat species with an archipelago-wide distribution, it is important to determine the population size on each island and connectivity between islands. We used 18 nuclear microsatellite loci and one mitochondrial gene from 339 individuals collected from 1988-2020 to evaluate genetic diversity, population structure and estimate effective population size on the Islands of Hawai'i, Maui, O'ahu, and Kaua'i. Genetic differentiation occurred between Hawai'i and Maui, both of which were differentiated from O'ahu and Kaua'i. The population on Maui presents the greatest per-island genetic diversity, consistent with their hypothesized status as the original founding population. A signature of isolation by distance was detected between islands, with contemporary migration analyses indicating limited gene flow in recent generations, and male-biased sex dispersal within Maui. Historical and long-term estimates of genetic effective population sizes were generally larger than contemporary estimates, although estimates of contemporary genetic effective population size lacked upper bounds in confidence intervals for Hawai'i and Kaua'i. Contemporary genetic effective population sizes were smaller on O'ahu and Maui. We also detected evidence of past bottlenecks on all islands with the exception of Hawai'i. Our study provides population-level estimates for the genetic diversity and geographic structure of 'ope'ape'a, that could be used by agencies tasked with wildlife conservation in Hawai'i.

A Genome for Bidens hawaiensis: A Member of a Hexaploid Hawaiian Plant Adaptive Radiation.

The plant genus Bidens (Asteraceae or Compositae; Coreopsidae) is a species-rich and circumglobally distributed taxon. The 19 hexaploid species endemic to the Hawaiian Islands are considered an iconic example of adaptive radiation, of which many are imperiled and of high conservation concern. Until now, no genomic resources were available for this genus, which may serve as a model system for understanding the evolutionary genomics of explosive plant diversification. Here, we present a high-quality reference genome for the Hawai'i Island endemic species B. hawaiensis A. Gray reconstructed from long-read, high-fidelity sequences generated on a Pacific Biosciences Sequel II System. The haplotype-aware, draft genome assembly consisted of ~6.67 Giga bases (Gb), close to the holoploid genome size estimate of 7.56 Gb (±0.44 SD) determined by flow cytometry. After removal of alternate haplotigs and contaminant filtering, the consensus haploid reference genome was comprised of 15 904 contigs containing ~3.48 Gb, with a contig N50 value of 422 594. The high interspersed repeat content of the genome, approximately 74%, along with hexaploid status, contributed to assembly fragmentation. Both the haplotype-aware and consensus haploid assemblies recovered >96% of Benchmarking Universal Single-Copy Orthologs. Yet, the removal of alternate haplotigs did not substantially reduce the proportion of duplicated benchmarking genes (~79% vs. ~68%). This reference genome will support future work on the speciation process during adaptive radiation, including resolving evolutionary relationships, determining the genomic basis of trait evolution, and supporting ongoing conservation efforts.

Conservation of magnetite biomineralization genes in all domains of life and implications for magnetic sensing.

Animals use geomagnetic fields for navigational cues, yet the sensory mechanism underlying magnetic perception remains poorly understood. One idea is that geomagnetic fields are physically transduced by magnetite crystals contained inside specialized receptor cells, but evidence for intracellular, biogenic magnetite in eukaryotes is scant. Certain bacteria produce magnetite crystals inside intracellular compartments, representing the most ancient form of biomineralization known and having evolved prior to emergence of the crown group of eukaryotes, raising the question of whether magnetite biomineralization in eukaryotes and prokaryotes might share a common evolutionary history. Here, we discover that salmonid olfactory epithelium contains magnetite crystals arranged in compact clusters and determine that genes differentially expressed in magnetic olfactory cells, contrasted to nonmagnetic olfactory cells, share ancestry with an ancient prokaryote magnetite biomineralization system, consistent with exaptation for use in eukaryotic magnetoreception. We also show that 11 prokaryote biomineralization genes are universally present among a diverse set of eukaryote taxa and that nine of those genes are present within the Asgard clade of archaea Lokiarchaeota that affiliates with eukaryotes in phylogenomic analysis. Consistent with deep homology, we present an evolutionary genetics hypothesis for magnetite formation among eukaryotes to motivate convergent approaches for examining magnetite-based magnetoreception, molecular origins of matrix-associated biomineralization processes, and eukaryogenesis.

Taro Genome Assembly and Linkage Map Reveal QTLs for Resistance to Taro Leaf Blight.

Taro (Colocasia esculenta) is a food staple widely cultivated in the humid tropics of Asia, Africa, Pacific and the Caribbean. One of the greatest threats to taro production is Taro Leaf Blight caused by the oomycete pathogen Phytophthora colocasiae Here we describe a de novo taro genome assembly and use it to analyze sequence data from a Taro Leaf Blight resistant mapping population. The genome was assembled from linked-read sequences (10x Genomics; ∼60x coverage) and gap-filled and scaffolded with contigs assembled from Oxford Nanopore Technology long-reads and linkage map results. The haploid assembly was 2.45 Gb total, with a maximum contig length of 38 Mb and scaffold N50 of 317,420 bp. A comparison of family-level (Araceae) genome features reveals the repeat content of taro to be 82%, >3.5x greater than in great duckweed (Spirodela polyrhiza), 23%. Both genomes recovered a similar percent of Benchmarking Universal Single-copy Orthologs, 80% and 84%, based on a 3,236 gene database for monocot plants. A greater number of nucleotide-binding leucine-rich repeat disease resistance genes were present in genomes of taro than the duckweed, ∼391 vs. ∼70 (∼182 and ∼46 complete). The mapping population data revealed 16 major linkage groups with 520 markers, and 10 quantitative trait loci (QTL) significantly associated with Taro Leaf Blight disease resistance. The genome sequence of taro enhances our understanding of resistance to TLB, and provides markers that may accelerate breeding programs. This genome project may provide a template for developing genomic resources in other understudied plant species.

Insights into the Evolutionary History of the Hawaiian Bidens (Asteraceae) Adaptive Radiation Revealed Through Phylogenomics.

Hawaiian plant radiations often result in lineages with exceptionally high species richness and extreme morphological and ecological differentiation. However, they typically display low levels of genetic variation, hindering the use of classic DNA markers to resolve their evolutionary histories. Here we utilize a phylogenomic approach to generate the first generally well-resolved phylogenetic hypothesis for the evolution of the Hawaiian Bidens (Asteraceae) adaptive radiation, including refined initial colonization and divergence time estimates. We sequenced the chloroplast genome (plastome) and nuclear ribosomal complex for 18 of the 19 endemic species of Hawaiian Bidens and 4 outgroup species. Phylogenomic analyses based on the concatenated dataset (plastome and nuclear) resulted in identical Bayesian and Maximum Likelihood trees with high statistical support at most nodes. Estimates from dating analyses were similar across datasets, with the crown group emerging ~1.76-1.82 Mya. Biogeographic analyses based on the nuclear and concatenated datasets indicated that colonization within the Hawaiian Islands generally followed the progression rule with 67-80% of colonization events from older to younger islands, while only 53% of events followed the progression rule in the plastome analysis. We find strong evidence for nuclear-plastome conflict indicating a potentially important role for hybridization in the evolution of the group. However, incomplete lineage sorting cannot be ruled out due to the small number of independent loci analyzed. This study contributes new insights into species relationships and the biogeographic history of the explosive Hawaiian Bidens adaptive radiation.

Draft Genome of the Rice Coral Montipora capitata Obtained from Linked-Read Sequencing.

The rice coral, Montipora capitata, is widely distributed throughout the Indo-Pacific and comprises one of the most important reef-building species in the Hawaiian Islands. Here, we describe a de novo assembly of its genome based on a linked-read sequencing approach developed by 10x Genomics. The final draft assembly consisted of 27,870 scaffolds with a N50 size of 186 kb and contained a fairly complete set (81%) of metazoan benchmarking (BUSCO) genes. Based on haploid assembly size (615 Mb) and read k-mer profiles, we estimated the genome size to fall between 600 and 700 Mb, although the high fraction of repetitive sequence introduced considerable uncertainty. Repeat analysis indicated that 42% of the assembly consisted of interspersed, mostly unclassified repeats, and almost 3% tandem repeats. We also identified 36,691 protein-coding genes with a median coding sequence length of 807 bp, together spanning 7% of the assembly. The high repeat content and heterozygosity of the genome proved a challenging scenario for assembly, requiring additional steps to merge haplotypes and resulting in a higher than expected fragmentation at the scaffold level. Despite these challenges, the assembly turned out to be comparable in most quality measures to that of other available coral genomes while being considerably more cost-effective, especially with respect to long-read sequencing methods. Provided high-molecular-weight DNA is available, linked-read technology may thus serve as a valuable alternative capable of providing quality genome assemblies of nonmodel organisms.

Hawaiian picture-winged Drosophila exhibit adaptive population divergence along a narrow climatic gradient on Hawaii Island.

Anthropogenic influences on global processes and climatic conditions are increasingly affecting ecosystems throughout the world.Hawaii Island's native ecosystems are well studied and local long-term climatic trends well documented, making these ecosystems ideal for evaluating how native taxa may respond to a warming environment.This study documents adaptive divergence of populations of a Hawaiian picture-winged Drosophila, D. sproati, that are separated by only 7 km and 365 m in elevation.Representative laboratory populations show divergent behavioral and physiological responses to an experimental low-intensity increase in ambient temperature during maturation. The significant interaction of source population by temperature treatment for behavioral and physiological measurements indicates differential adaptation to temperature for the two populations.Significant differences in gene expression among males were mostly explained by the source population, with eleven genes in males also showing a significant interaction of source population by temperature treatment.The combined behavior, physiology, and gene expression differences between populations illustrate the potential for local adaptation to occur over a fine spatial scale and exemplify nuanced response to climate change.

Symbiont type and environmental factors affect transcriptome-wide gene expression in the coral Montipora capitata.

Reef-building corals may harbor genetically distinct lineages of endosymbiotic dinoflagellates in the genus Symbiodinium, which have been shown to affect important colony properties, including growth rates and resilience against environmental stress. However, the molecular processes underlying these differences are not well understood. In this study, we used whole transcriptome sequencing (RNA-seq) to assess gene expression differences between 27 samples of the coral Montipora capitata predominantly hosting two different Symbiodinium types in clades C and D. The samples were further characterized by their origin from two field sites on Hawai'i Island with contrasting environmental conditions. We found that transcriptome-wide gene expression profiles clearly separated by field site first, and symbiont clade second. With 273 differentially expressed genes (DEGs, 1.3% of all host transcripts), symbiont clade had a measurable effect on host gene expression, but the effect of field site proved almost an order of magnitude higher (1,957 DEGs, 9.6%). According to SNP analysis, we found moderate evidence for host genetic differentiation between field sites (F ST = 0.046) and among corals harboring alternative symbiont clades (F ST = 0.036), suggesting that site-related gene expression differences are likely due to a combination of local adaptation and acclimatization to environmental factors. The correlation between host gene expression and symbiont clade may be due to several factors, including host genotype or microhabitat selecting for alternative clades, host physiology responding to different symbionts, or direct modulation of host gene expression by Symbiodinium. However, the magnitude of these effects at the level of transcription was unexpectedly small considering the contribution of symbiont type to holobiont phenotype.

Anthropogenic habitat alteration leads to rapid loss of adaptive variation and restoration potential in wild salmon populations.

Phenotypic variation is critical for the long-term persistence of species and populations. Anthropogenic activities have caused substantial shifts and reductions in phenotypic variation across diverse taxa, but the underlying mechanism(s) (i.e., phenotypic plasticity and/or genetic evolution) and long-term consequences (e.g., ability to recover phenotypic variation) are unclear. Here we investigate the widespread and dramatic changes in adult migration characteristics of wild Chinook salmon caused by dam construction and other anthropogenic activities. Strikingly, we find an extremely robust association between migration phenotype (i.e., spring-run or fall-run) and a single locus, and that the rapid phenotypic shift observed after a recent dam construction is explained by dramatic allele frequency change at this locus. Furthermore, modeling demonstrates that continued selection against the spring-run phenotype could rapidly lead to complete loss of the spring-run allele, and an empirical analysis of populations that have already lost the spring-run phenotype reveals they are not acting as sustainable reservoirs of the allele. Finally, ancient DNA analysis suggests the spring-run allele was abundant in historical habitat that will soon become accessible through a large-scale restoration (i.e., dam removal) project, but our findings suggest that widespread declines and extirpation of the spring-run phenotype and allele will challenge reestablishment of the spring-run phenotype in this and future restoration projects. These results reveal the mechanisms and consequences of human-induced phenotypic change and highlight the need to conserve and restore critical adaptive variation before the potential for recovery is lost.

A High-Quality, Long-Read De Novo Genome Assembly to Aid Conservation of Hawaii's Last Remaining Crow Species.

Abstract: Genome-level data can provide researchers with unprecedented precision to examine the causes and genetic consequences of population declines, which can inform conservation management. Here, we present a high-quality, long-read, de novo genome assembly for one of the world's most endangered bird species, the 'Alala (Corvus hawaiiensis; Hawaiian crow). As the only remaining native crow species in Hawai'i, the 'Alala survived solely in a captive-breeding program from 2002 until 2016, at which point a long-term reintroduction program was initiated. The high-quality genome assembly was generated to lay the foundation for both comparative genomics studies and the development of population-level genomic tools that will aid conservation and recovery efforts. We illustrate how the quality of this assembly places it amongst the very best avian genomes assembled to date, comparable to intensively studied model systems. We describe the genome architecture in terms of repetitive elements and runs of homozygosity, and we show that compared with more outbred species, the 'Alala genome is substantially more homozygous. We also provide annotations for a subset of immunity genes that are likely to be important in conservation management, and we discuss how this genome is currently being used as a roadmap for downstream conservation applications.

Phylogenetic Relationships, Breeding Implications, and Cultivation History of Hawaiian Taro (Colocasia Esculenta) Through Genome-Wide SNP Genotyping.

Taro, Colocasia esculenta, is one of the world's oldest root crops and is of particular economic and cultural significance in Hawai'i, where historically more than 150 different landraces were grown. We developed a genome-wide set of more than 2400 high-quality single nucleotide polymorphism (SNP) markers from 70 taro accessions of Hawaiian, South Pacific, Palauan, and mainland Asian origins, with several objectives: 1) uncover the phylogenetic relationships between Hawaiian and other Pacific landraces, 2) shed light on the history of taro cultivation in Hawai'i, and 3) develop a tool to discriminate among Hawaiian and other taros. We found that almost all existing Hawaiian landraces fall into 5 monophyletic groups that are largely consistent with the traditional Hawaiian classification based on morphological characters, for example, leaf shape and petiole color. Genetic diversity was low within these clades but considerably higher between them. Population structure analyses further indicated that the diversification of taro in Hawai'i most likely occurred by a combination of frequent somatic mutation and occasional hybridization. Unexpectedly, the South Pacific accessions were found nested within the clades mainly composed of Hawaiian accessions, rather than paraphyletic to them. This suggests that the origin of clades identified here preceded the colonization of Hawai'i and that early Polynesian settlers brought taro landraces from different clades with them. In the absence of a sequenced genome, this marker set provides a valuable resource towards obtaining a genetic linkage map and to study the genetic basis of phenotypic traits of interest to taro breeding such as disease resistance.

De novo metatranscriptome assembly and coral gene expression profile of Montipora capitata with growth anomaly.

BACKGROUND: Scleractinian corals are a vital component of coral reef ecosystems, and of significant cultural and economic value worldwide. As anthropogenic and natural stressors are contributing to a global decline of coral reefs, understanding coral health is critical to help preserve these ecosystems. Growth anomaly (GA) is a coral disease that has significant negative impacts on coral biology, yet our understanding of its etiology and pathology is lacking. In this study we used RNA-seq along with de novo metatranscriptome assembly and homology assignment to identify coral genes that are expressed in three distinct coral tissue types: tissue from healthy corals ("healthy"), GA lesion tissue from diseased corals ("GA-affected") and apparently healthy tissue from diseased corals ("GA-unaffected"). We conducted pairwise comparisons of gene expression among these three tissue types to identify genes and pathways that help us to unravel the molecular pathology of this coral disease. RESULTS: The quality-filtered de novo-assembled metatranscriptome contained 76,063 genes, of which 13,643 were identified as putative coral genes. Overall gene expression profiles of coral genes revealed high similarity between healthy tissue samples, in contrast to high variance among diseased samples. This indicates GA has a variety of genetic effects at the colony level, including on seemingly healthy (GA-unaffected) tissue. A total of 105 unique coral genes were found differentially expressed among tissue types. Pairwise comparisons revealed the greatest number of differentially expressed genes between healthy and GA-affected tissue (93 genes), followed by healthy and GA-unaffected tissue (33 genes), and GA-affected and -unaffected tissue (7 genes). The putative function of these genes suggests GA is associated with changes in the activity of genes involved in developmental processes and activation of the immune system. CONCLUSION: This is one of the first transcriptome-level studies to investigate coral GA, and the first metatranscriptome assembly for the M. capitata holobiont. The gene expression data, metatranscriptome assembly and methodology developed through this study represent a significant addition to the molecular information available to further our understanding of this coral disease.

Geo-Referenced, Abundance Calibrated Ocean Distribution of Chinook Salmon (Oncorhynchus tshawytscha) Stocks across the West Coast of North America.

Understanding seasonal migration and localized persistence of populations is critical for effective species harvest and conservation management. Pacific salmon (genus Oncorhynchus) forecasting models predict stock composition, abundance, and distribution during annual assessments of proposed fisheries impacts. Most models, however, fail to account for the influence of biophysical factors on year-to-year fluctuations in migratory distributions and stock-specific survival. In this study, the ocean distribution and relative abundance of Chinook salmon (O. tshawytscha) stocks encountered in the California Current large marine ecosystem, U.S.A were inferred using catch-per-unit effort (CPUE) fisheries and genetic stock identification data. In contrast to stock distributions estimated through coded-wire-tag recoveries (typically limited to hatchery salmon), stock-specific CPUE provides information for both wild and hatchery fish. Furthermore, in contrast to stock composition results, the stock-specific CPUE metric is independent of other stocks and is easily interpreted over multiple temporal or spatial scales. Tests for correlations between stock-specific CPUE and stock composition estimates revealed these measures diverged once proportional contributions of locally rare stocks were excluded from data sets. A novel aspect of this study was collection of data both in areas closed to commercial fisheries and during normal, open commercial fisheries. Because fishing fleet efficiency influences catch rates, we tested whether CPUE differed between closed area (non-retention) and open area (retention) data sets. A weak effect was indicated for some, but not all, analyzed cases. Novel visualizations produced from stock-specific CPUE-based ocean abundance facilitates consideration of how highly refined, spatial and genetic information could be incorporated in ocean fisheries management systems and for investigations of biogeographic factors that influence migratory distributions of fish.

Effects of historical climate change, habitat connectivity, and vicariance on genetic structure and diversity across the range of the red tree vole (Phenacomys longicaudus) in the Pacific Northwestern United States.

Phylogeographical analyses conducted in the Pacific Northwestern United States have often revealed concordant patterns of genetic diversity among taxa. These studies demonstrate distinct North/South genetic discontinuities that have been attributed to Pleistocene glaciation. We examined phylogeographical patterns of red tree voles (Phenacomys longicaudus) in western Oregon by analysing mitochondrial control region sequences for 169 individuals from 18 areas across the species' range. Cytochrome b sequences were also analysed from a subset of our samples to confirm the presence of major haplotype groups. Phylogenetic network analyses suggested the presence of two haplotype groups corresponding to northern and southern regions of P. longicaudus' range. Spatial genetic analyses (samova and Genetic Landscape Shapes) of control region sequences demonstrated a primary genetic discontinuity separating northern and southern sampling areas, while a secondary discontinuity separated northern sampling areas into eastern and western groups divided by the Willamette Valley. The North/South discontinuity likely corresponds to a region of secondary contact between lineages rather than an overt barrier. Although the Cordilleran ice sheet (maximum approximately 12,000 years ago) did not move southward to directly affect the region occupied by P. longicaudus, climate change during glaciation fragmented the forest landscape that it inhabits. Signatures of historical fragmentation were reflected by positive associations between latitude and variables such as Tajima's D and patterns associated with location-specific alleles. Genetic distances between southern sampling areas were smaller, suggesting that forest fragmentation was reduced in southern vs. northern regions.

Temporal changes in allele frequencies and low effective population size in greater prairie-chickens.

The number of greater prairie-chickens in Wisconsin has decreased by 91% since 1932. The current population of approximately 1500 birds exists primarily in four isolated management areas. In previous studies of the Wisconsin populations we documented low levels of genetic variation at microsatellite loci and the mitochondrial DNA control region. Here we investigate changes in genetic structure between the four management areas in Wisconsin over the last 50 years. We estimated the harmonic mean effective population size (Ne) over the last 50 years by comparing allele frequencies from the early 1950s with those from contemporary samples. Using a pseudo-likelihood approach that accounted for migration, estimates of Ne (15-32 prairie-chickens within each management area) were 10 times lower than census numbers from booming-ground counts. These low estimates of Ne are consistent with increased habitat fragmentation and an increase in genetic isolation between management areas over the last 50 years. The reduction of gene flow between areas has reduced Ne, increased genetic drift and, consequently, reduced genetic variation. These results have immediate consequences for the conservation of the prairie-chicken, and highlight the importance of how mating systems and limited dispersal may exacerbate the loss of genetic variation in fragmented populations.