Aron D. Katz

Bio: Aron D. Katz is an academic researcher from University of Illinois at Urbana–Champaign. The author has contributed to research in topics: Chaetotaxy & Biological dispersal. The author has an hindex of 4, co-authored 13 publications receiving 97 citations. Previous affiliations of Aron D. Katz include Illinois Natural History Survey & Engineer Research and Development Center.

At the confluence of vicariance and dispersal: Phylogeography of cavernicolous springtails (Collembola: Arrhopalitidae, Tomoceridae) codistributed across a geologically complex karst landscape in Illinois and Missouri.

Abstract: The processes of vicariance and dispersal are central to our understanding of diversification, yet determining the factors that influence these processes remains a significant challenge in evolutionary biology. Caves offer ideal systems for examining the mechanisms underlying isolation, divergence, and speciation. Intrinsic ecological differences among cavernicolous organisms, such as the degree of cave dependence, are thought to be major factors influencing patterns of genetic isolation in caves. Using a comparative phylogeographic approach, we employed mitochondrial and nuclear markers to assess the evolutionary history of two ecologically distinct groups of terrestrial cave-dwelling springtails (Collembola) in the genera Pygmarrhopalites (Arrhopalitidae) and Pogonognathellus (Tomoceridae) that are codistributed in caves throughout the Salem Plateau-a once continuous karst region, now bisected by the Mississippi River Valley in Illinois and Missouri. Contrasting phylogeographic patterns recovered for troglobiotic Pygmarrhopalites sp. and eutroglophilic Pogonognathellus sp. suggests that obligate associations with cave habitats can restrict dispersal across major geographic barriers such as rivers and valleys, but may also facilitate subterranean dispersal between neighboring cave systems. Pygmarrhopalites sp. populations spanning the Mississippi River Valley were estimated to have diverged 2.9-4.8 Ma, which we attribute to vicariance resulting from climatic and geological processes involved in Mississippi River Valley formation beginning during the late Pliocene/early Pleistocene. Lastly, we conclude that the detection of many deeply divergent, morphologically cryptic, and microendemic lineages highlights our poor understanding of microarthropod diversity in caves and exposes potential conservation concerns.

Taxonomic review and phylogenetic analysis of fifteen North American Entomobrya (Collembola, Entomobryidae), including four new species

Abstract: The chaetotaxy of 15 species of eastern North American Entomobrya is redescribed in order to determine potential characters for the diagnosis of cryptic lineages and evaluate the diagnostic and phylogenetic utility of chaetotaxy. As a result, four new species (Entomobrya citrensis Katz & Soto-Adames, sp. n., Entomobrya jubata Katz & Soto-Adames, sp. n., Entomobrya neotenica Katz & Soto-Adames, sp. n. and Entomobrya unifasciata Katz & Soto-Adames, sp. n.) are described, and new diagnoses are provided for Entomobrya assuta Folsom, Entomobrya atrocincta Schott, Entomobrya decemfasciata (Packard), Entomobrya ligata Folsom, Entomobrya multifasciata (Tullberg), and Entomobrya quadrilineata (Bueker). Furthermore, previously undocumented levels of intraspecific variation in macrosetal pattern are reported, tempering the exclusive use of chaetotaxy for species delimitation. Phylogenetic relationships, estimated using both morphological and molecular data, indicate that Entomobrya is likely paraphyletic. The phylogenies also suggest that unreliable character homology, likely fostered by Entomobrya's profusion of macrosetae, may limit the phylogenetic utility of chaetotaxy in groups characterized by an abundance of dorsal macrosetae.

Environmental DNA is effective in detecting the federally threatened Louisiana Pinesnake (Pituophis ruthveni)

Abstract: Successful conservation of rare, threatened, or endangered (RTE) species is dependent upon rapid and accurate assessment of their distribution and abundance. However, assessments are challenging as RTE species typically exist as numerically small populations in often fragmented habitats and can possess complex natural histories. Environmental DNA (eDNA) analysis may provide a rapid, cost‐effective means of assessing RTE species presence/absence in viable habitat patches. We evaluated the efficacy of eDNA surveillance for the Louisiana Pinesnake (Pituophis ruthveni), an elusive, semi‐fossorial, nonvenomous colubroid snake endemic to Louisiana and Texas, USA, that has dramatically declined in both distribution and abundance. We developed two quantitative polymerase chain reaction (qPCR) assays that target the mitochondrial cytochrome c oxidase subunit I (COI) and mitochondrially encoded ATP synthase membrane subunit 6 (ATP6) genes. We validated each assay in silico, in vitro, and in situ, and investigated the influence of eDNA extraction method and genetic marker on assay performance. Both assays were highly sensitive and successfully detected the Louisiana Pinesnake under artificial and field conditions, including bedding samples collected from captive snake enclosures (100%), soil samples from Louisiana Pinesnake release sites (100%), and soil samples from sites where Louisiana Pinesnakes were documented via radio telemetry (45%). Although differences between genetic markers were negligible, assay performance was strongly influenced by eDNA extraction method. Informed by our results, we discuss methodological and environmental factors influencing Louisiana Pinesnake eDNA detection and quantification, broader implications for management and conservation of the Louisiana Pinesnake and other terrestrial reptiles and provide recommendations for future research. We suggest that eDNA surveys can more effectively assess Louisiana Pinesnake occupancy than conventional sampling, highlighting the need for comprehensive eDNA monitoring initiatives to better identify suitable habitat that will promote persistence of this imperiled species going forward.

Spatial light interference microscopy (SLIM)

Abstract: We present SLIM, a new optical method measuring optical pathlength changes of 0.3 nm spatially and 0.03nm temporally. SLIM combines two classic ideas in light imaging: Zernike’s phase contrast microscopyand Gabor’s holography.

Physical volcanology and structural development of Sierra Negra Volcano, Isabela Island, Galapagos Archipelago

Abstract: Sierra Negra is the most voluminous of the western Galapagos shields and exhibits many unusual morphologic features: extensive lower flank apron, steep upper flanks, a broad summit plateau, a large complex caldera, ubiquitous occurrence of aa, and radial and circumferential fissures. A field-based investigation of the volcano was conducted in order to establish the distribution and characteristics of eruptive zones and associated flow fields and to construct a volcano-wide surface flow stratigraphy. Geochronologic data were used to determine the age of the units and, combined with flow-volume calculations, to estimate both the historic and total volcano eruption rates. Ninety-one kilometers of radial and circumferential fissures were mapped and grouped into four eruptive zones which form a volcano-wide east-northeast–trending rift system that deflects around the caldera. The eruptive zones are restricted spatially and temporally and document long-term changes in the volcano's development. Long, fluid lava flows are broadly distributed among five ages, resulting in a subdued flank profile by the development of an extensive lower flank apron around the volcano. Ten historical eruptions have occurred, with eruption rates of 44 to 248 m3/s and an average growth rate of 12 × 106 m3/yr. Age determinations of lava flows by 14C and cosmogenic 3He range from 400 to 6900 yr. The total volcano growth rate is estimated to be 1 × 106 m3/yr. These results confirm the young age of Sierra Negra lavas and the validity of the relative ages determined from stratigraphic study. In total, the volcano has undergone over 90% resurfacing in the past 4500 yr. The summit of Sierra Negra is entirely occupied by a shallow, elliptical (7 × 10 km) caldera. Near-vertical ring faults circumscribe the summit and expose 100 to 140 m of lava flows. Subparallel sets of caldera growth faults cut the western and southern caldera walls and are not associated with eruptive activity. The inclination of remnant magnetism and the attitudes of the flows exposed in the caldera walls indicate that the lavas have not been appreciably deformed nor have they been intruded by dikes or sills. The caldera interior is structurally complex and contains a 14-km-long, C-shaped sinuous ridge, composed of a complex set of normally faulted blocks with inward dipping (20°–60°) flow tops. The sinuous ridge is interpreted to have formed gradually as the caldera floor pivoted in a trap door fashion, jammed its western edge, and then fractured in several places, concomitant with the long-term vertical and lateral growth of the volcano. A regional tectonic stress field superimposed upon the Galapagos platform appears to have exerted primary control on the location of Sierra Negra, including the early development of the east-northeast rift system. Intervolcano stresses have controlled the distribution of eruptive zones only where significant subaerial overlap of adjacent volcanoes occurs. Large volume, high discharge rate eruptions from fissures along the east-northeast rift system are responsible for the development of an extensive coastal apron, flow stacking at mid-flank elevations, and generally subdued slopes in comparison to other western Galapagos volcanoes. The summit caldera and underlying magma chamber are subordinate in influencing the distribution of lower flank stress but dominate the development of the summit stress field and orientation of eruptive fissures. The absence of summit deformation, together with the ubiquitous occurrence of short stubby summit flows, indicates that the steep upper flanks are constructional in origin.

Phylogenomics Resolves The Timing And Pattern Of Insect Evolution: Supplementary File Archives.

Abstract: Toward an insect evolution resolution Insects are the most diverse group of animals, with the largest number of species. However, many of the evolutionary relationships between insect species have been controversial and difficult to resolve. Misof et al. performed a phylogenomic analysis of protein-coding genes from all major insect orders and close relatives, resolving the placement of taxa. The authors used this resolved phylogenetic tree together with fossil analysis to date the origin of insects to ~479 million years ago and to resolve long-controversial subjects in insect phylogeny. Science, this issue p. 763 The phylogeny of all major insect lineages reveals how and when insects diversified. Insects are the most speciose group of animals, but the phylogenetic relationships of many major lineages remain unresolved. We inferred the phylogeny of insects from 1478 protein-coding genes. Phylogenomic analyses of nucleotide and amino acid sequences, with site-specific nucleotide or domain-specific amino acid substitution models, produced statistically robust and congruent results resolving previously controversial phylogenetic relations hips. We dated the origin of insects to the Early Ordovician [~479 million years ago (Ma)], of insect flight to the Early Devonian (~406 Ma), of major extant lineages to the Mississippian (~345 Ma), and the major diversification of holometabolous insects to the Early Cretaceous. Our phylogenomic study provides a comprehensive reliable scaffold for future comparative analyses of evolutionary innovations among insects.

Towards a global synthesis of Collembola knowledge – challenges and potential solutions

Abstract: Collembola are among the most abundant and diverse soil microarthropods, which are found in almost all (semi)terrestrial environments and often serve as model organisms in empirical studies. Diverse data collected on the biology and ecology of Collembola over the last century are waiting for synthesis studies, while developing technologies may facilitate generation of new knowledge. Collembola research in 2020 is entering the stage of global synthesis and in this opinion paper we address the main challenges that the community of collembologists is facing on this avenue. We first discuss the present status and social context of Collembola taxonomy and the potential use of novel technologies to describe new species. We then focus on aspects of community ecology, reviewing the processes of dispersal, environmental and biotic filtering, from the spatial scale of microhabitat to the globe. We also discuss the involvement of Collembola in ecosystem processes and which proxies, such as functional traits, can be used to predict the functional roles of species. Finally, we provide recommendations on how we can improve community data collection by using standard methods and better data handling practices. We call for (1) integrating morphological descriptions with high-resolution photographs and genetic barcodes for species descriptions and developing of user friendly software and machine learning approaches to facilitate deposition of structured taxonomic knowledge on web platforms; (2) multiscale studies on biodiversity distribution and community processes, especially including dispersal mechanisms; (3) recording and sharing functional, not only morphological, trait data in controlled experiments and field surveys; (4) knowledge synthesis and meta-analysis studies on the topics of ecosystem roles of Collembola, conservation of its diversity, feeding behaviour, protection mechanisms and dispersal of different Collembola species, and effects of land use and climate change on collembolan communities; (5) joint efforts in covering the gaps in Collembola knowledge, especially in underexplored regions (predominantly tropics and subtropics) using standard methodologies; (6) data sharing and its integration in open structured databases. We believe that Collembola studies could make use of new technologies and ongoing changes in society. To facilitate the progress across these research topics by 2040, we have established #GlobalCollembola, a distributed-effort community-driven initiative that aims to provide open and global data on Collembola taxonomic and genetic diversity, abundance, traits and literature and to coordinate global efforts in covering the key knowledge gaps.

Ultra-large alignments using Phylogeny-aware Profiles

Abstract: Many biological questions, including the estimation of deep evolutionary histories and the detection of remote homology between protein sequences, rely upon multiple sequence alignments (MSAs) and phylogenetic trees of large datasets. However, accurate large-scale multiple sequence alignment is very difficult, especially when the dataset contains fragmentary sequences. We present UPP, an MSA method that uses a new machine learning technique - the Ensemble of Hidden Markov Models - that we propose here. UPP produces highly accurate alignments for both nucleotide and amino acid sequences, even on ultra-large datasets or datasets containing fragmentary sequences. UPP is available at this https URL