Biology subjects

Van Dam, M. H.

Publications and source records attributed to Van Dam, M. H..

4 recordsLinked to original sources

bioRxiv2021

How the Easter Egg Weevils Got Their Spots: Phylogenomics reveals Müllerian Mimicry in Pachyrhynchus (Coleoptera, Curculionidae).

The evolutionary origins of mimicry in the Easter Egg weevil, Pachyrhynchus, have fascinated researchers since first noted more than a century ago by Alfred Russel Wallace. Mullerian mimicry, or mimicry in which two or more distasteful species look similar, is widespread throughout the animal kingdom. Given the varied but discrete color patterns in Pachyrhynchus, this genus presents one of the best opportunities to study the evolution of both perfect and imperfect mimicry. We analyzed more than 10,000 UCE loci using a novel partitioning strategy to resolve the relationships of closely related species in the genus. Our results indicate that many of the mimetic color patterns observed in sympatric species are due to convergent evolution. We suggest that this convergence is driven by frequency-dependent selection.

evolutionary biology↗

bioRxiv2020

The Easter Egg Weevil (Pachyrhynchus) genome reveals synteny in Coleoptera across 200 million years of evolution

Patterns of genomic architecture across insects remain largely undocumented or decoupled from a broader phylogenetic context. For instance, it is unknown whether translocation rates differ between insect orders? We address broad scale patterns of genome architecture across Insecta by examining synteny in a phylogenetic framework from open source insect genomes. To accomplish this, we add a chromosome level genome to a crucial lineage, Coleoptera. Our assembly of the Pachyrhynchus sulphureomaculatus genome is the first chromosome scale genome for the hyperdiverse Phytophaga lineage and currently the largest insect genome assembled to this scale. The genome is significantly larger than those of other weevils, and this increase in size is caused by repetitive elements. Our results also indicate that, among beetles, there are instances of long-lasting (>200 Ma) localization of genes to a particular chromosome with few translocation events. While some chromosomes have a paucity of translocations, intra-chromosomal synteny was almost absent, with gene order thoroughly shuffled along a chromosome. To place our findings in an evolutionary context, we compared syntenic patterns across Insecta. We find that synteny largely scales with clade age, with younger clades, such as Lepidoptera, having especially high synteny. However, we do find subtle differences in the maintenance of synteny and its rate of decay among the insect orders.

genomics↗

bioRxiv2019

Genomic characterization and curation of UCEs improves species tree reconstruction.

Ultraconserved genomic elements (UCEs), are generally treated as independent loci in phylogenetic analyses. The identification pipeline for UCE probes is agnostic to genetic identity, only selecting loci that are highly conserved, single copy, without repeats, and of a particular length. Here we characterized UCEs from 12 phylogenomic studies across the animal tree of life, from birds to marine invertebrates. We found that within vertebrate lineages, UCEs are mostly intronic and intergenic, while in invertebrates, the majority are in exons. We then curated 4 different sets of UCE markers by genomic category from 5 different studies including; birds, mammals, fish, Hymenoptera (ants, wasps and bees) and Coleoptera (beetles). Of genes captured by UCEs, we find that many are represented by 2 or more UCEs, corresponding to non-overlapping segments of a single gene. We considered these UCEs to be non-independent, merged all UCEs that belonged to a particular gene, constructed gene and species trees, and then evaluated the subsequent effect of merging co-genic UCEs on gene and species tree reconstruction. Average bootstrap support for merged UCE gene trees were significantly improved across all datasets. Increased loci length appears to drive this increase in bootstrap support. Additionally, we found that gene trees generated from merged UCEs were more accurate than those generated by unmerged and randomly merged UCEs, based on our simulation study. This modest degree of UCE characterization and curation impacts downstream analyses and demonstrates the advantages of incorporating basic genomic characterizations into phylogenomic analyses.

evolutionary biology↗

bioRxiv2019

Environmental Niche Adaptation Revealed Through Fine Scale Phenological Niche Modeling

AimPhenology, the temporal response of a population to its climate, is a crucial behavioral trait shared across life on earth. How species adapt their phenologies to climate change is poorly understood but critical in understanding how species will respond to future change. We use a group of flies (Rhaphiomidas) endemic to the North American deserts to understand how species adapt to changing climatic conditions. Here we explore a novel approach for taxa with constrained phenologies aimed to accurately model their environmental niche and relate this to phenological and morphological adaptations in a phylogenetic context. TaxonInsecta, Diptera, Mydidae, Rhaphiomidas LocationNorth America, Mojave, Sonoran and Chihuahuan Deserts. MethodsWe gathered geographical and phenological occurrence data for the entire genus Rhaphiomidas, and, estimated a time calibrated phylogeny. We compared Daymet derived temperature values for a species adult occurrence period (phenology) with those derived from WorldClim data that is partitioned by month or quarter to examine what effect using more precise data has on capturing a species environmental niche. We then examined to what extent phylogenetic signal in phenological traits, climate tolerance and morphology can inform us about how species adapt to different environmental regimes. ResultsWe found that the Bioclim temperature data, which are averages across monthly intervals, poorly represent the climate windows to which adult flies are actually adapted. Using temporally-relevant climate data, we show that many species use a combination of morphological and phenological changes to adapt to different climate regimes. There are also instances where species changed only phenology to track a climate type or only morphology to adapt to different environments. Main ConclusionsWithout using a fine-scale phenological data approach, identifying environmental adaptations could be misleading because the data do not represent the conditions the animals are actually experiencing. We find that fine-scale phenological niche models are needed when assessing taxa that have a discrete phenological window that is key to their survival, accurately linking environment to morphology and phenology. Using this approach, we show that Rhaphiomidas use a combination of niche tracking and adaptation to persist in new niches. Modeling the effect of phenology on such species niches will be critical for better predictions of how these species might respond to future climate change.

evolutionary biology↗