Matthew L Niemiller

Matthew L Niemiller
University of Alabama in Huntsville | UAH · Department of Biological Sciences

Ph.D.

About

262
Publications
53,079
Reads
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2,194
Citations
Additional affiliations
August 2017 - present
University of Alabama in Huntsville
Position
  • Professor (Assistant)
August 2016 - present
University of Illinois, Urbana-Champaign
Position
  • Associate Ecologist
August 2014 - July 2016
University of Illinois, Urbana-Champaign
Position
  • PostDoc Position
Education
August 2006 - August 2011
University of Tennessee
Field of study
  • Ecology & Evolutionary BIology
August 2003 - May 2006

Publications

Publications (262)
Chapter
Preorder here: https://www.press.jhu.edu/books/title/12872/cave-biodiversity This chapter and the book It will be available in mid-2022. We examined how the environment, and particularly habitat and geologic structure, influence evolutionary pathways leading toward subterranean specialization. Through the widespread application of molecular appr...
Chapter
Preorder here: https://www.press.jhu.edu/books/title/12872/cave-biodiversity This chapter and the book It will be available in mid-2022. China supports the highest diversity of cavefishes in the world. With 148 known species, this accounts for one-third of all cavefishes globally. In this chapter, we review Chinese cavefish diversity, distributi...
Article
Full-text available
Due to their limited geographic distributions and specialized ecologies, cave species are often highly endemic and can be especially vulnerable to habitat degradation within and surrounding the cave systems they inhabit. We investigated the evolutionary history of the West Virginia Spring Salamander (Gyrinophilus subterraneus), estimated the popula...
Article
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Cryptic species present particular challenges to biodiversity conservation, as true species diversity and distributional boundaries remain obscured. However, modern molecular tools have afforded unparalleled opportunities to elucidate cryptic species, define their distributions, and, ultimately, develop conservation interventions to extend their ev...
Article
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Subterranean ecosystems are among the most widespread environments on Earth, yet we still have poor knowledge of their biodiversity. To raise awareness of subterranean ecosystems, the essential services they provide, and their unique conservation challenges, 2021 and 2022 were designated International Years of Caves and Karst. As these ecosystems h...
Article
Brazil’s caves, home to diverse species and minerals, were stripped of protections by a recent presidential decree.
Preprint
Pollinators are imperiled by global declines that can impair 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. Environm...
Article
Conservation and education outreach programs often highlight charismatic species or species of economic or ecological importance. However, without appreciable connections to nature, the foundation necessary to empathize with these programs is insufficient. While many students are familiar with charismatic organisms, such as large mammals or sea tur...
Article
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The 15th UN Convention on Biological Diversity (CBD) (COP15) will be held in Kunming, China in October 2021. Historically, CBDs and other multilateral treaties have either alluded to or entirely overlooked the subterranean biome. A multilateral effort to robustly examine, monitor, and incorporate the subterranean biome into future conservation targ...
Article
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The Mammoth Cave System in the Interior Low Plateau karst region in central Kentucky, USA is a global hotspot of cave-limited biodiversity, particularly terrestrial species. We searched the literature, museum accessions, and database records to compile an updated list of troglobiotic and stygobiotic species for the Mammoth Cave System and compare o...
Article
Full-text available
The 15th UN Convention on Biological Diversity (CBD) (COP15) will be held in Kunming, China in October 2021. Historically, CBDs and other multilateral treaties have either alluded to or entirely overlooked the subterranean biome. A multilateral effort to robustly examine, monitor, and incorporate the subterranean biome into future conservation targ...
Article
Full-text available
Male combat in snakes is a sexually dimorphic trait in adults, primarily expressed during breeding periods, and under certain conditions confers reproductive advantages to winners by way of priority-of-access to sexually active females. Male combat is ubiquitous in North American pitvipers, including A. contortrix, and in most circumstances is coin...
Article
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Subterranean habitats represent focal habitats in many conservation strategies; however, these environments are some of the most difficult to sample. New sampling methods, such as environmental DNA (eDNA), show promise to improve stygobiont detection, but sources of sampling bias are poorly understood. Therefore, we determined the factors affecting...
Article
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We sequenced the mitochondrial genomes of one spring-dwelling (Crangonyx forbesi) and four groundwater amphipods (Bactrurus brachycaudus, Stygobromus allegheniensis, S. pizzinii, and S. t. potomacus) from eastern North America using a shotgun sequencing approach on an Illumina HiSeq 4000 (Illumina, San Diego, CA). All five mitochondrial genomes enc...
Article
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The study of spring- and subterranean-associated microsnail species in the Appalachian karst region has focused disproportionately on the northern Appalachian Valley and Ridge (AVR), leaving many areas in the southern Appalachians unexplored. Consequently, biological inventories of subterranean habitats have been initiated in the southern AVR, part...
Article
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Many taxonomic groups have successfully exploited groundwater environments and adapted to a subterranean (stygobiotic) existence. Among these groups are freshwater gastropods (stygosnails), which represent a widespread and taxonomically diverse component of groundwater ecosystems in the United States and Mexico; no stygosnails are known from Canada...
Article
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Many questions relevant to conservation decision-making are characterized by extreme uncertainty due to lack of empirical data and complexity of the underlying ecologic processes, leading to a rapid increase in the use of structured protocols to elicit expert knowledge. Published ecologic applications often employ a modified Delphi method, where ex...
Article
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Over 1,500 caves have been documented in North Carolina, however, cave fauna in the Blue Ridge Mountains and Piedmont regions of North Carolina have been overlooked historically compared to the cave-rich karst terrains in the Appalachian Valley and Ridge and Interior Low Plateau to the west. Here, we provide the first comprehensive faunal list of c...
Article
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The conservation and management of subterranean biodiversity is hindered by a lack of knowledge on the true distributions for many species, e.g., the Wallacean shortfall. In recent years, several studies have demonstrated the potential of environmental DNA (eDNA) as an effective approach to detect and monitor biodiversity, including rare, threatene...
Article
Five decades ago, a landmark paper in Science titled The Cave Environment heralded caves as ideal natural experimental laboratories in which to develop and address general questions in geology, ecology, biogeography, and evolutionary biology. Although the 'caves as laboratory' paradigm has since been advocated by subterranean biologists, there are...
Article
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We provide an annotated checklist of species recorded from caves and other subterranean habitats in the state of Georgia, USA. We report 281 species (228 invertebrates and 53 vertebrates), including 51 troglobionts (cave-obligate species), from more than 150 sites (caves, springs, and wells). Endemism is high; of the troglobionts, 17 (33 % of those...
Article
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The Caney Mountain cave crayfish (Orconectes stygocaneyi) is one of North America’s rarest crayfish, endemic to one cave in southern Missouri, USA. The species is listed as “critically imperiled” by Missouri, and “threatened” by the American Fisheries Society. Previously, only 15 crayfish have been observed in Mud Cave, and only two have been colle...
Article
Cave adaptation has evolved repeatedly across the Tree of Life, famously leading to pigmentation and eye degeneration and loss, yet its macroevolutionary implications remain poorly understood. We use the North American amblyopsid fishes, a family spanning a wide degree of cave adaptation, to examine the impact of cave specialization on the modes an...
Article
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A new species of cave snail (Littorinimorpha: Cochliopidae) in the genus Antrorbis is described from the dark zone of two caves in the Appalachian Valley and Ridge province in eastern Tennessee, United States. The Tennessee Cavesnail, Antrorbis tennesseensis Perez, Shoobs, Gladstone, & Niemiller, sp. nov. is distinguished from its only known congen...
Article
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The Alabama Cave Shrimp Palaemonias alabamae Smalley, 1961 is a federally endangered cave shrimp endemic to just four cave systems within and near the greater Huntsville metropolitan area in Madison County, Alabama USA. It is one of two described atyid cave shrimp in the Interior Low Plateau karst region. Here we report the discovery of a new popul...
Article
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In this contribution, the aspects of reptile and amphibian speciation that emerged from research performed over the past decade are reviewed. First, this study assesses how patterns and processes of speciation depend on knowing the taxonomy of the group in question, and discuss how integrative taxonomy has contributed to speciation research in thes...
Article
In light of recent alarming trends in human population growth, climate change, and other environmental modifications, a "Warning to humanity" manifesto was published in BioScience in 2017. This call reiterated most of the ideas originally expressed by the Union of Concerned Scientists in 1992, including the fear that we are "pushing Earth's ecosyst...
Preprint
Full-text available
Cave adaptation has led to unique sensory specializations to compensate for the lack of visual cues in aphotic subterranean habitats. As the role of vision is reduced or disappears, other sensory modalities become hypertrophied allowing cave-adapted organisms to successfully detect and interact with their surrounding environment. The array of aquat...
Article
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Molecular studies have recently led to the detection of many cryptic species complexes within morphologically ambiguous species formerly undescribed by the scientific community. Organisms such as land snails are at a particularly higher risk of species misidentification and misinterpretation, in that gastropod systematics are based almost entirely...
Chapter
Salamanders are the only tetrapod vertebrates capable of having an exclusively hypogean life cycle. In contrast to the great number of salamanders that temporarily inhabit caves, only 13 species of obligate cave-dwellers are known. Troglobiotic salamanders are found in North America (12 species in the family Plethodontidae) and Europe (one species...
Poster
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Despite the economic and environmental importance of subterranean ecosystems, there is a fundamental lack of knowledge regarding the distribution and abundance of the many species that occupy caves and other subterranean habitats. Subterranean habitats can be extraordinarily challenging to access and navigate, and even when biologically sampled, sm...
Article
Cave adaptation leads to unique anatomical specializations in many taxonomic groups. As the role of vision is reduced or disappears in a subterranean environment, other specializations arise to allow the organism to successfully detect and interact with their environment. A suite of unique, convergent phenotypes associated with subterranean adaptat...
Article
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Lungless salamanders in the family Plethodontidae exhibit an impressive array of life history strategies and occur in a diversity of habitats, including caves. However, relationships between life history, habitat, and body size remain largely unresolved. During an ongoing study on the demography and life history of the paedomorphic, cave-obligate B...
Preprint
Full-text available
Speciation processes have long been inferred from phylogenetic, phylogeographic, and biogeographic pattern-driven perspectives. Now much current speciation research is attempting to more directly describe the underlying processes and mechanisms of divergence leading to speciation. Ideally, researchers should integrate both process-and pattern-based...
Preprint
Full-text available
Speciation processes have long been inferred from phylogenetic, phylogeographic, and biogeographic pattern-driven perspectives. Now much current speciation research is attempting to more directly describe the underlying processes and mechanisms of divergence leading to speciation. Ideally, researchers should integrate both process- and pattern-base...
Article
Full-text available
The pseudoscorpion genus Hesperochernes presently includes 19 species, 17 of which are endemic to North America. On this continent, most species in the genus have been found in association with bats or rodents, and six species are known exclusively from subterranean habitats. Three species are distributed south of the Great Lakes in the eastern par...
Conference Paper
Full-text available
Cavefishes are a distinctive group of animals restricted to subterranean environments for at least for part of their lives. Their level of troglomorphism differentiates them into groups: stygobionts (troglomorphic) and stygophiles/stygoxenes (non-troglomorphic). China is home to the greatest diversity of cavefishes in the world, with more than 76 e...
Article
Full-text available
Environmental DNA represents a potentially cost-effective method for detection of rare and cryptic species, for which traditional sampling can be logistically costly. We tested species-specific probe-based assays to detect eDNA for the federally threatened eastern massasauga rattlesnake and the causative agent of snake fungal disease, Ophidiomyces...
Article
Full-text available
Effective conservation and management of biodiversity is limited by a lack of critical knowledge on species’ distributions and abundances. This problem is particularly exacerbated for species living in habitats that are exceptionally difficult to access or survey, such as ground- water habitats. Environmental DNA (eDNA) represents a rapid, noninvas...
Article
Full-text available
Cave-obligate (troglobiotic) land snails are among the most understudied taxa inhabiting cave systems because of their small size and cryptic nature. Other than locality records and general descriptions of species’ morphology, information regarding most cave snail taxa is minimal. Given the importance of land snails as indicator species and as impo...
Poster
Full-text available
ABSTRACT: Earth is facing a rapid decline of biodiversity within its natural systems, which has critical implications on ecosystem functions and services. Successful conservation efforts to slow this decline rely on the ability to monitor species and understand their ecological role. Such efforts are often hindered by a lack of knowledge regarding...
Chapter
We review significant conservation and management legislation, policies, and other actions that have been implemented or proposed to protect and conserve subterranean biodiversity in Europe, North America, Central America, and South America. In particular, we focus on legislation at the national and international levels that has been passed or prop...
Article
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The only mudpuppy (Caudata: Proteidae) known to occur in the Tennessee Valley of the Interior Highlands and Southern Appalachians is the Common Mudpuppy (Necturus maculosus). Necturus maculosus is not known to co-occur with any other congeners. Here, we report evidence that an additional Necturus occurs in the Hiwassee River, a tributary of the Ten...
Article
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The transition from carnivory to omnivory is poorly understood. The ability to feed at more than one trophic level theoretically increases an animal’s 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 i...
Conference Paper
Full-text available
The Appalachian Valley and Ridge (AVR) region of East Tennessee (USA) is one of the most cave-rich areas of the state, with approximately 1,470 caves in a 6,379 km 2 area. Despite decades of exploration, only 5.1% of caves in the area were biologically inventoried prior to 2013 and basic data on species distributions were lacking. This sampling gap...
Conference Paper
Full-text available
Of the >50,000 caves reported in the United States, nearly 1,140 cave-restricted animals (troglobionts) have been described. One of the most biodiverse karst areas in the United States is the area near the shared boundaries of Tennessee, Alabama, and Georgia (TAG) in the Appalachian Valley and Ridge (AVR) ecoregion. Large sampling gaps in the AVR l...
Poster
Full-text available
A diverse snail fauna exists within the caves of central and eastern North America, represented by over 95 genera and 260 terrestrial and aquatic species. In most freshwater and surface environments, gastropods play significant roles in many food webs and provide a diverse array of ecosystem services, including: accelerating decomposition of leaf l...
Article
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Cambarus cryptodytes (Dougherty Plain Cave Crayfish) is an obligate inhabitant of groundwater habitats (i.e., a stygobiont) with troglomorphic adaptations in the Floridan aquifer system of southwestern Georgia and adjacent Florida panhandle, particularly in the Dougherty Plain and Marianna Lowlands. Documented occurrences of Dougherty Plain Cave Cr...
Preprint
Full-text available
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...
Article
Full-text available
Divergent host use has long been suspected to drive population differentiation and speciation in plant-feeding insects. Evaluating the contribution of divergent host use to genetic differentiation can be difficult, however, as dispersal limitation and population structure may also influence patterns of genetic variation. In this study, we use doubl...
Article
Full-text available
In the central and eastern United States, cavefishes have been known historically only from the Interior Low Plateau and Ozarks karst regions. Previously, cavefishes were unknown from the Appalachians karst region, which extends from southeastern New York southwestward into eastern Tennessee, northwestern Georgia, and northeastern Alabama. Here we...