Biology subjects

Diamond, S. E.

Publications and source records attributed to Diamond, S. E..

5 recordsLinked to original sources

bioRxiv2023

Single-fly assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life

Long-read sequencing is driving rapid progress in genome assembly across all major groups of life, including species of the family Drosophilidae, a longtime model system for genetics, genomics, and evolution. We previously developed a cost-effective hybrid Oxford Nanopore (ONT) long-read and Illumina short-read sequencing approach and used it to assemble 101 drosophilid genomes from laboratory cultures, greatly increasing the number of genome assemblies for this taxonomic group. The next major challenge is to address the laboratory culture bias in taxon sampling by sequencing genomes of species that cannot easily be reared in the lab. Here, we build upon our previous methods to perform amplification-free ONT sequencing of single wild flies obtained either directly from the field or from ethanol-preserved specimens in museum collections, greatly improving the representation of lesser studied drosophilid taxa in whole-genome data. Using Illumina Novaseq X Plus and ONT P2 sequencers with R10.4.1 chemistry, we set a new benchmark for inexpensive hybrid genome assembly at US $150 per genome while assembling genomes from as little as 35 ng of genomic DNA from a single fly. We present 183 new genome assemblies for 179 species as a resource for drosophilid systematics, phylogenetics, and comparative genomics. Of these genomes, 62 are from pooled lab strains and 121 from single adult flies. Despite the sample limitations of working with small insects, most single-fly diploid assemblies are comparable in contiguity (>1Mb contig N50), completeness (>98% complete dipteran BUSCOs), and accuracy (>QV40 genome-wide with ONT R10.4.1) to assemblies from inbred lines. We present a well-resolved multi-locus phylogeny for 360 drosophilid and 4 outgroup species encompassing all publicly available (as of August 2023) genomes for this group. Finally, we present a Progressive Cactus whole-genome, reference-free alignment built from a subset of 298 suitably high-quality drosophilid genomes. The new assemblies and alignment, along with updated laboratory protocols and computational pipelines, are released as an open resource and as a tool for studying evolution at the scale of an entire insect family.

evolutionary biology↗

bioRxiv2023

Local climate change velocities explain multidirectional range shifts in a North American butterfly assemblage

Species are often expected to shift their distributions poleward to evade warming climates. However, from 18 years of fixed transect monitoring data on 88 species of butterfly in the midwestern United States, we show that butterflies are shifting their centroids in all directions, except towards the region that is warming the fastest (southeast). Butterflies shifted their centroids at a mean rate of 4.87 km yr-1. The rate of centroid shift was significantly associated with local climate change velocity (temperature and precipitation), but not with mean climate change velocity throughout the species ranges. Surprisingly, the centroid shift was also unrelated to species traits expected to mediate the shift response including thermal niche breadth (range of climates butterflies experience throughout their distribution) and wingspan (often used as metric for dispersal capability). Contrasting with a number of previous studies, we observed relatively high phylogenetic signal in the rate and direction species shifted their centroids, suggesting that evolutionary history helps to explain multidirectional range shift responses and that some groups of species will be better able to shift their ranges than others. This research shows important signatures of multidirectional range shifts (latitudinal and longitudinal) and uniquely shows that local climate change velocities are more important in driving range shifts than the mean climate change velocity throughout a species entire range.

ecology↗

bioRxiv2022

Linking physiology to ecosystem function: how vulnerable are different functional groups to climate change?

O_LIThe resilience of ecosystem function under global climate change is governed by individual species vulnerabilities and the functional groups they contribute to (e.g. decomposition, primary production, pollination, primary, secondary and tertiary consumption). Yet it remains unclear whether species that contribute to different functional groups, which underpin ecosystem function, differ in their vulnerability to climate change. C_LIO_LIIt is important to examine if functional group vulnerability differs across space (e.g. tropical vs temperate latitudes) to determine if some regions will be more vulnerable to loss of ecosystem function than others, and to examine whether localized effects of particular community compositions override global patterns of functional group vulnerability. C_LIO_LIWe used existing upper thermal limit data across a range of terrestrial species (N = 1,743) to calculate species warming margins (degrees distance between a species upper thermal limit and the maximum environmental temperature they inhabit), as a metric of climate change vulnerability, to determine whether species that comprise different functional groups exhibit differential vulnerability to climate change, and if vulnerability trends change across geographic space. C_LIO_LIWe found that primary producers had the broadest warming margins across the globe ( = 21.85 {degrees}C) and that tertiary consumers had the narrowest warming margins ( = 4.37 {degrees}C), where vulnerability tended to increase with trophic level. C_LIO_LISpecies that contribute towards primary production were more vulnerable in low-latitude than mid-latitude regions, but warming margins across all other functional groups did not differ across regions when evolutionary history was considered. However, when evolutionary history was excluded from the analyses (as closely related species often play similar functional roles within ecosystems demonstrating true variation in functional group warming margins) we found that pollinators are more vulnerable in mid-latitude regions and that primary producers are more vulnerable in low-latitude environments. C_LIO_LIThis study provides a critical first step in linking individual species vulnerabilities with whole ecosystem responses to climate change. C_LI

ecology↗

bioRxiv2020

In a nutshell, a reciprocal transplant experiment reveals local adaptation and fitness trade-offs in response to urban evolution in an acorn-dwelling ant

Urban-driven evolution is widely evident, but whether these changes confer fitness benefits and thus represent cases of adaptive urban evolution is less clear. We performed a multi-year field reciprocal transplant experiment of acorn-dwelling ants across urban and rural environments. Fitness trade-offs via survival were consistent with local adaptation: we found a survival advantage of the home treatments compared to the away treatments. Seasonal bias in survival was consistent with evolutionary patterns of gains and losses in thermal tolerance traits across the urbanization gradient, such that rural ants in the urban environment were more vulnerable in the summer, putatively due to low heat tolerance and urban ants in the rural environment were more vulnerable in winter, putatively due to an evolved loss of cold tolerance. The results for fitness via fecundity were more complex. Fecundity differences were present in the rural environment, but not the urban environment, and could reflect mismatched cues for the seasonal production of reproductives. To broadly contextualize our results, we performed a multi-species meta-analysis of urban adaptive evolution studies and found general support for local adaptation. The rural adaptation signal was stronger than for urban adaptation, consistent with the relative differences in time for adaptation to occur.

evolutionary biology↗

bioRxiv2019

Evolution, not transgenerational plasticity, explains the divergence of acorn ant thermal tolerance across an urban-rural temperature cline

Disentangling the mechanisms of phenotypic shifts in response to environmental change is critical, and although studies increasingly disentangle phenotypic plasticity from evolutionary change, few explore the potential role for transgenerational plasticity in this context. Here, we evaluate the potential role that transgenerational plasticity plays in phenotypic divergence of acorn ants in response to urbanization. F2 generation worker ants (offspring of lab-born queens) exhibited similar divergence among urban and rural populations as F1 generation worker ants (offspring of field-born queens) indicating that evolutionary differentiation rather than transgenerational plasticity was responsible for shifts towards higher heat tolerance and diminished cold tolerance in urban acorn ants. Hybrid matings between urban and rural populations provided further insight into the genetic architecture of thermal adaptation. Heat tolerance of hybrids more resembled the urban-urban pure type, whereas cold tolerance of hybrids more resembled the rural-rural pure type. As a consequence, thermal tolerance traits in this system appear to be influenced by dominance rather than being purely additive traits, and heat and cold tolerance might be determined by separate genes. Though transgenerational plasticity does not explain divergence of acorn ant thermal tolerance, its role in divergence of other traits and across other urbanization gradients merits further study.

evolutionary biology↗