Remarkably High Repeat Content in the Genomes of Sparrows: The Importance of Genome Assembly Completeness for Transposable Element Discovery

Genome Biology and Evolution, Год журнала: 2024, Номер 16(4)

Опубликована: Апрель 1, 2024

Abstract Transposable elements (TE) play critical roles in shaping genome evolution. Highly repetitive TE sequences are also a major source of assembly gaps making it difficult to fully understand the impact these on host genomes. The increased capacity long-read sequencing technologies span highly regions promises provide new insights into patterns activity across diverse taxa. Here we report generation contiguous reference genomes using PacBio and Omni-C for three species Passerellidae sparrow. We compared assemblies chromosome-level sparrow nine other generated variety short- technologies. All based were longer (range: 1.12 1.41 Gb) than short-read (0.91 1.08 length was strongly correlated with amount repeat content. Repeat content Bell's (31.2% genome) highest level ever reported within order Passeriformes, which comprises over half avian diversity. levels (79.2% 93.7%) found W chromosome relative genome. Finally, show that proliferation different classes varied even among similar These support dynamic model expansion contraction clade where TEs once thought be fairly depauperate static. Our work highlights how resolution difficult-to-assemble transform our understanding

Язык: Английский

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Salinity Acclimation Induces Reduced Energy Metabolism, Osmotic Pressure Regulation and Transcriptional Reprogramming in Hypotrichida Ciliate Gastrostyla setifera

Journal of Ocean University of China, Год журнала: 2024, Номер 23(2), С. 539 - 549

Опубликована: Апрель 1, 2024

Язык: Английский

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Assessing the evidence for treating developmental plasticity and phenotypic flexibility as different phenomena

Functional Ecology, Год журнала: 2024, Номер unknown

Опубликована: Июнь 5, 2024

Abstract Phenotypic plasticity has long played a central role in eco‐evolutionary theory, but it was not until 20 years ago that proposed the term encompasses two distinct phenomena—developmental and phenotypic flexibility. While this terminology since been adopted by some, question of whether they are phenomena remains contentious both frequently lumped under umbrella ‘plasticity.’ Here, we treat dichotomy between developmental flexibility as hypothesis, put forth set predictions follow from review support for hypothesis literature. We predict that, if result separate phenomena, developmentally plastic phenotypically flexible traits should differ in: (1) environmental context which evolve, (2) their mechanisms regulation, (3) costs production, (4) how selection acts on them (5) influence population's evolutionary trajectory. In general, most evidence supports treating much to be learned, few studies have specifically investigated potential differences. particular, explorations well trait production reversal needed. Given hypothesized link plasticity, resiliency face rapid change, is an urgent topic will further our understanding evolution across contexts. Read free Plain Language Summary article Journal blog.

Язык: Английский

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Maintenance of local adaptation despite gene flow in a coastal songbird

Evolution, Год журнала: 2022, Номер 76(7), С. 1481 - 1494

Опубликована: Июнь 14, 2022

Adaptation to local environments is common in widespread species and the basis of ecological speciation. The song sparrow (Melospiza melodia) a widespread, polytypic passerine that occurs shrubland habitats throughout North America. We examined population structure two parapatric subspecies inhabit different environments: Atlantic (M. m. atlantica), coastal specialist, eastern melodia), generalist. These populations lacked clear mitochondrial structure, yet birds formed distinct nuclear genetic cluster. found weak overall genomic differentiation between these subspecies, suggesting either recent divergence, extensive gene flow, or combination thereof. There was steep cline at transition habitats, consistent with isolation by environment, not distance. A phenotype under divergent selection, bill size, varied amount ancestry transitional areas, but larger size maintained regardless ancestry, further supporting role for selection maintenance subspecies. Demographic modeling suggested divergence history limited flow followed secondary contact, which has emerged as theme adaptive across taxa.

Язык: Английский

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Genomic differentiation and local adaptation on a microgeographic scale in a resident songbird

Molecular Ecology, Год журнала: 2020, Номер 29(22), С. 4295 - 4307

Опубликована: Сен. 26, 2020

Abstract Elucidating forces capable of driving species diversification in the face gene flow remains a key goal evolutionary biology. Song sparrows, Melospiza melodia, occur as 25 subspecies diverse habitats across North America, are among continent's most widespread vertebrate species, and exemplary many highly variable for which conservation locally adapted populations may be critical to their range‐wide persistence. We focus here on six morphologically distinct resident San Francisco Bay region, including three salt‐marsh endemics residents upland riparian adjacent Bay. used reduced‐representation sequencing generate 2,773 SNPs explore genetic differentiation, spatial population structure, demographic history. Clustering separated individuals from each subspecies, indicating subtle differentiation at microgeographic scales. Evidence limited low nucleotide diversity all further supports hypothesis isolation populations. suggest that natural selection genotypes salt marsh environments changes demography over past century have acted concert drive patterns reported here. Our results offer evidence specialization polytypic bird long discussed model sympatric speciation rapid adaptation, they support conserving persistence similarly species.

Язык: Английский

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Remarkably high repeat content in the genomes of sparrows: the importance of genome assembly completeness for transposable element discovery

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Окт. 31, 2023

ABSTRACT Transposable elements (TE) play critical roles in shaping genome evolution. However, the highly repetitive sequence content of TEs is a major source assembly gaps. This makes it difficult to decipher impact these on dynamics The increased capacity long-read sequencing technologies span regions should provide novel insights into patterns TE diversity. Here we report generation contiguous reference genomes using PacBio long read and Omni-C for three species sparrows family Passerellidae. To assess influence technology annotation, compared assemblies chromosome-level sparrow recently generated by Vertebrate Genomes Project nine other variety short- technologies. All based were longer length (range: 1.12-1.41 Gb) than short-read (0.91-1.08 Gb). Assembly was strongly correlated with amount repeat content, showing much higher levels typically reported avian order Passeriformes. Repeat Bell’s (31.2% genome) highest level date songbird more line woodpecker (order Piciformes) genomes. CR1 LINE retained from an expansion that occurred 25-30 million years ago most abundant song genome. Although five also exhibit evidence spike activity at ago, LTR stemming recent expansions species. LTRs uniquely deriving two peaks activity. Higher (79.2-93.7%) found W chromosome relative Z (20.7-26.5) or autosomes (16.1-30.9%). These support dynamic model transposable element contraction underpinning seemingly constrained small sized birds. Our work highlights how resolution difficult-to-assemble new promises transform our understanding

Язык: Английский

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The influence of spatially heterogeneous anthropogenic change on bill size evolution in a coastal songbird

Evolutionary Applications, Год журнала: 2020, Номер 14(2), С. 607 - 624

Опубликована: Окт. 6, 2020

Abstract Natural history collections provide an unparalleled resource for documenting population responses to past anthropogenic change. However, in many cases, traits measured on specimens may vary temporally response a number of different pressures or demographic processes. While teasing apart these drivers is challenging, approaches that integrate analyses spatial and temporal series can robust framework examining whether exhibit common ecological variation space time. We applied this approach analyze bill morphology California Savannah Sparrows ( Passerculus sandwichensis ). found surface area increased birds from higher salinity tidal marshes are hotter drier. Only the coastal subspecies, alaudinus, exhibited significant increase size through As with patterns variation, alaudinus populations occupying have become warmer drier over century greatest increases area. also negative correlation between total evaporative water loss (TEWL) estimated observed could result reduction up 16.2% daily losses. Together, were consistent hypothesis larger bills favored freshwater‐limited environments as mechanism dissipating heat, reducing reliance cooling, increasing conservation. With museum increasingly being leveraged understand global change, work highlights importance considering influence axes change integrating better specific human impacts

Язык: Английский

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Evolutionary divergence and adaptive capacity in morphologically distinct song sparrow subspecies

Conservation Genetics, Год журнала: 2023, Номер 24(6), С. 921 - 932

Опубликована: Июль 31, 2023

Язык: Английский

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Spatial variation in population genomic responses to over a century of anthropogenic change within a tidal marsh songbird

Global Change Biology, Год журнала: 2024, Номер 30(1)

Опубликована: Янв. 1, 2024

Abstract Combating the current biodiversity crisis requires accurate documentation of population responses to human‐induced ecological change. However, our ability pinpoint human activities is often limited analysis populations studied well after fact. Museum collections preserve a record anthropogenic change that can provide critical baseline data on patterns genetic diversity, connectivity, and structure prior onset perturbation. Here, we leverage spatially replicated time series specimens document genomic destruction nearly 90% coastal habitats occupied by Savannah sparrow ( Passerculus sandwichensis ) in California. We sequenced 219 sparrows collected from 1889 2017 across state California using an exome capture approach. Spatial–temporal analyses diversity found amount habitat lost was not predictive loss. Sparrow southern historically exhibited lower levels experienced most significant temporal declines diversity. Despite experiencing greatest loss, San Francisco Bay area remained relatively high. This potentially related observed increase gene flow into Area other populations. While may have minimized declines, also immigration inland freshwater‐adapted tidal marsh led erosion divergence at loci associated with adaptation. Shifting through response loss thus contribute negative fitness consequences outbreeding depression. Together, results underscore importance tracing trajectories multiple over address issues fundamental conservation concern.

Язык: Английский

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Integrating spatial analyses of genomic and physiological data to understand avian responses to environmental change

Integrative and Comparative Biology, Год журнала: 2024, Номер unknown

Опубликована: Июнь 3, 2024

Projected rates of climate change over the next century are expected to force species shift ranges, adapt or acclimate evade extinction. Predicting which these scenarios may be most likely is a central challenge for conserving biodiversity in immediate future. Modeling frameworks that take advantage intraspecific variation across environmental gradients can particularly important meeting this challenge. While space-for-time approaches essential climatic and genomic modeling approaches, mechanistic models incorporate ecological physiology data into assessing vulnerabilities rarely include variation. A major reason gap general lack empirical on geographic avian physiological traits. In review, we outline evidence processes shaping We use example evaporative water loss underscore research even traits cooling costs birds. demonstrate how shifting focus facilitate greater integration with emerging genomics approaches. Finally, steps an integrative approach advance understanding adaptation within species. Addressing knowledge gaps outlined review will contribute improved predictive framework synthesizes environmental, morphological, physiological, assess specific warming planet.

Язык: Английский

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