Despite broad interest in and study of subterranean biodiversity, substantial knowledge gaps remain, impeding conservation efforts. Addressing these knowledge gaps is a focus of my research program, and includes biological inventories of understudied karst regions, studies of demography and life history, and a variety of genetic-based studies – all of which lead to the discovery of new subterranean species. I use population genetic methods to assess genetic diversity within populations, ascertain connectivity among demes, and identify lineages and cryptic conservation units in taxa often threatened by anthropogenic activities. Current projects use NGS approaches, such as RADseq, to study and test hypotheses on population dynamics in cave beetles and investigate the efficacy of environmental DNA (eDNA) as a tool to document and monitor aquatic subterranean communities, using subterranean crustaceans as a model. eDNA has the potential to provide valuable insights into cryptic species diversity and especially for biodiversity monitoring in subterranean habitats that otherwise would be extremely difficult to sample by traditional means.
Invertebrates, which comprise the overwhelming majority of subterranean biodiversity, are often neglected in conservation, with less than 10% of subterranean taxa having been subjected to IUCN Red List assessments. I conduct status assessments for subterranean species, identifying factors associated with extinction risk in subterranean biodiversity, including biological and anthropogenic correlates.
CRYPTIC SPECIES DELIMITATION AND CONSERVATION
A major challenge facing the conservation and management of biodiversity is that a signifiant portion of biodiversity remains to be discovered and described. This problem is manifested in subterranean organisms where species delimitation is often hampered by morphological convergence, lack of morphological differentiation, and lack of data on reproductive isolation between groups. Consequently, our understanding of species boundaries is poor for several groups of organisms, compromising our ability to study and conserve these taxa. I have taken an integrated approach to species delimitation using multilocus data and newly developed methodologies to infer species boundaries in a morphological invariable cavefish species (Typhlichthys subterraneus) and evaluate these new methods empirically (Niemiller et al. 2012). In addition to examining subtle morphological variation in this species complex with the prospect of describing several new species, I am also applying these new approaches in an integrative framework in other subterranean taxa to examine temporal and biogeographic patterns of diversification.
The discovery of cryptic species has important conservation implications for several reasons, with one of the most important being accurate assessments of the conservation status of species (Niemiller & Fitzpatrick 2008; Niemiller et al. 2013). In general, few cryptic lineages identified in genetic studies have been formally described (i.e., the Linnean shortfall), and even fewer have been subjected to conservation assessments. This is especially significant in cryptic species complexes in which the nominal species is already of conservation concern. I conducted IUCN Red List and NatureServe conservation assessments of recently delimited lineages in a cavefish species of conservation concern (Niemiller et al. 2012) to determine the conservation status of each cryptic lineage and identify lineages at greatest risk of extinction (Niemiller et al. 2013). Although the nominal species is not threatened range-wide, most lineages are at an elevated risk of extinction from at least ten documented threats that vary in scope and severity among lineages. Conservation assessments, even for taxa yet to be assigned a Latin binomial, are critical for conservation. Unfortunately, many subterranean species have not been subjected to conservation assessments. I am working with taxonomic experts for several subterranean groups to not only search for hidden diversity, but also conduct conservation assessments to assist in the preservation and management of subterranean biodiversity.