Biology subjects

Niemiller, M. L.

Publications and source records attributed to Niemiller, M. L..

5 recordsLinked to original sources

bioRxiv2026

Competition among freshwater clades explains cave colonization in blind cavefishes

Flatfishes display the most dramatic asymmetric body plan in vertebrates, yet whether this rare innovation evolved once (flatfish monophyly, FM) or multiple times (flatfish polyphyly, FP) has remained contentious. A recent genome-wide study supported FP by placing Psettodes, the earliest-diverging flatfish lineage, among symmetric relatives within Carangaria, the clade that also includes billfishes, jacks, mahi-mahi, and barracudas. Subsequent work traced this to base-composition artifacts and inadequate substitution modeling. Here we revisit the question using whole-genome phylogenomic and synteny data from 17 carangarian species spanning flatfishes and carangarian relatives. We contribute three new chromosome-level assemblies, including the first for Psettodes. Nucleotide-based coalescent analyses (e.g., ROADIES, CASTER) yield strong support for FM, with Psettodes sister to all other flatfishes. Microsynteny analyses built from conserved gene-order blocks corroborate this result: topology tests, cluster-profile counts, and rearrangement-based trees favor FM over two competing FP topologies. Macrosynteny, based on chromosome-scale rearrangements, yields a more mixed signal, with support for FM depending on the metric and taxon-sampling scheme. We interpret this scale-dependent pattern in the context of the explosive post-Cretaceous radiation of Carangaria. The short intervals between speciation events that characterize rapid radiations appear to have left sufficient signal in fine-grained microsyntenic rearrangements, while chromosome-scale rearrangements were too rare to consistently resolve these closely spaced splits. When integrated with evidence from conserved developmental mechanisms active during metamorphosis, the stage at which flatfish asymmetry first emerges, and from the exceptionally complete fossil record, our multi-scale genomic evidence supports a single evolutionary origin of flatfish asymmetry.

evolutionary biology↗

bioRxiv2023

Phylogenomics and Biogeography of North American Trechine Cave Beetles (Coleoptera: Carabidae)

Cave trechines beetles (Coleoptera: Carabidae: Trechini) are members of cave communities globally and important models for understanding the colonization of caves, adaptation to cave life, and the diversification of cave-adapted lineages. In eastern North America, cave trechines are the most species-rich group of terrestrial troglobionts, comprised of over 150 taxa in six genera with no extant surface members. Previous studies have hypothesized the climate change during the Pleistocene was a major driver of cave colonization and diversification in this and other temperate terrestrial cave fauna. However, our time-calibrated molecular phylogeny resulting from the analysis of 16,794 base pairs (bp) from 68 UCE loci for 45 species of the clade supports an alternative hypothesis whereby cave colonization of the surface ancestor of eastern North American cave trechines likely began in the middle Miocene in the Appalachians Ridge and Valley (APP) and dispersed into the Interior Low Plateau (ILP) in an east to west manner around 11.5 Mya. The APP served as a cradle for diversification and also as a bridge linking the southern Appalachians and Interior Low Plateau enabling the dispersal and subsequent diversification of these cave beetles. Major clades in our time-calibrated phylogeny attained their present-day geographic distributions by the early Miocene followed by multiple additional episodes of cave colonization and diversification occurring throughout the Pliocene and Pleistocene. The genera Neaphanops, Darlingtonea, Nelsonites, and Ameroduvalius were nested within specious genus Pseudanopthalmus supporting the hypothesis that these genera are derived Pseudanophtlamus. Moreover, while several morphologically-derived species groups of Pseudanopthalmus were recovered as monophyletic, others were not warranting future taxonomic and systematic research. The molecular systematics and biogeography of these unique cave beetles offer a model for other comparative evolutionary and ecological studies of troglobionts to further our understanding of factors driving speciation and biogeographic patterns.

ecology↗

bioRxiv2023

Comparative mitogenomic analysis of subterranean and surface amphipods (Crustacea, Amphipoda) with special reference to the family Crangonyctidae

Mitochondrial genomes play important roles in studying genome evolution, phylogenetic analyses, and species identification. Amphipods (Class Malacostraca, Order Amphipoda) are one of the most ecologically diverse crustacean groups occurring in a diverse array of aquatic and terrestrial environments globally, from freshwater streams and lakes to groundwater aquifers and the deep sea, but we have a limited understanding of how habitat influences the molecular evolution of mitochondrial energy metabolism. Subterranean amphipods likely experience different evolutionary pressures on energy management compared to surface-dwelling taxa that generally encounter higher levels of predation and energy resources and live in more variable environments. In this study, we compared the mitogenomes, including the 13 protein-coding genes involved in the oxidative phosphorylation (OXPHOS) pathway, of surface and subterranean amphipods to uncover potentially different molecular signals of energy metabolism between surface and subterranean environments in this diverse crustacean group. We compared base composition, codon usage, gene order rearrangement, conducted comparative mitogenomic and phylogenomic analyses, and examined evolutionary signals of 35 amphipod mitogenomes representing 13 families, with an emphasis on Crangonyctidae. Mitogenome size, AT content, GC-skew, gene order, uncommon start codons, location of putative control region (CR), length of rrnL and intergenic spacers differed between surface and subterranean amphipods. Among crangonyctid amphipods, the spring-dwelling Crangonyx forbesi exhibited a unique gene order, a long nad5 locus, longer rrnL and rrnS loci, and unconventional start codons. Evidence of directional selection was detected in several protein-encoding genes of the OXPHOS pathway in the mitogenomes of surface amphipods, while a signal of purifying selection was more prominent in subterranean species, which is consistent with the hypothesis that the mitogenome of surface-adapted species has evolved in response to a more energy demanding environment compared to subterranean amphipods. Overall, gene order, locations of non-coding regions, and base-substitution rates points to habitat as an important factor influencing the evolution of amphipod mitogenomes.

genomics↗

bioRxiv2021

BeeDNA: microfluidic environmental DNA metabarcoding as a tool for connecting plant and pollinator communities

Pollinators are imperiled by global declines that can reduce plant reproduction, erode essential ecosystem services and resilience, and drive economic losses. Monitoring pollinator biodiversity trends is key for adaptive conservation and management, but conventional surveys are often costly, time consuming, and require taxonomic expertise. Environmental DNA (eDNA) metabarcoding surveys are booming due to their rapidity, non-invasiveness, and cost efficiency. Microfluidic technology allows multiple primer sets from different markers to be used in eDNA metabarcoding for more comprehensive species inventories whilst minimizing biases associated with individual primer sets. We evaluated microfluidic eDNA metabarcoding for pollinator community monitoring by introducing a bumblebee colony to a greenhouse flower assemblage and sampling natural flower plots. We collected nectar draws, flower swabs, or whole flower heads from four flowering species, including two occurring in both the greenhouse and field. Samples were processed using two eDNA isolation protocols before amplification with 15 primer sets for two markers (COI and 16S). Microfluidic eDNA metabarcoding detected the target bumblebee and greenhouse insects as well as common regional arthropods. Pollinator detection was maximized using whole flower heads preserved in ATL buffer and extracted with a modified Qiagen(R) DNeasy protocol for amplification with COI primers. eDNA surveillance could enhance pollinator assessment by detecting protected and endangered species and being more applicable to remote, inaccessible locations, whilst reducing survey time, effort, and expense. Microfluidic eDNA metabarcoding requires optimization to address remaining efficacy concerns but this approach shows potential in revealing complex networks underpinning critical ecosystem functions and services, enabling more accurate assessments of ecosystem resilience.

ecology↗

bioRxiv2017

Evolution Of Coprophagy And Nutrient Absorption In A Cave Salamander

The transition from carnivory to omnivory is poorly understood. The ability to feed at more than one trophic level theoretically increases an animals fitness in a novel environment. Because of the absence of light and photosynthesis, most subterranean ecosystems are characterized by very few trophic levels, such that food scarcity is a challenge in many subterranean habitats. One strategy against starvation is to expand diet breadth. Grotto salamanders (Eurycea spelaea) are known to ingest bat guano deliberately, challenging the general understanding that salamanders are strictly carnivorous. Here we tested the hypothesis that grotto salamanders have broadened their diet related to cave adaptation and found that, although coprophagous behavior is present, salamanders are unable to acquire sufficient nutrition from bat guano alone. Our results suggest that the coprophagic behavior has emerged prior to physiological or gut biome adaptations.

animal behavior and cognition↗