How new species originate is a central question in evolutionary biology. We use a combination of techniques, including next generation DNA sequencing and whole genome assembly, high resolution computed tomography, cutting-edge phylogenetic, population genetic, and demographic tools, geological modeling, specimen collection, and geographic information systems to investigate the speciation process. We are particularly interested in freshwater fishes from the southeastern North American biodiversity hotspot, and PI Near has contributed to the discovery and naming of 11 new fish species from the southeastern United States and the Southern Ocean of Antarctica. Highlighted below are recent projects in this research domain.

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A major new research avenue in the lab focuses on geogenomics: putting genome-scale DNA sequence data in conversation with geological models to understand shared biological and Earth histories. From: 10.1126/science.add9791

High resolution computed tomography scans of Mirror Shiner (Notropis spectrunculus) illuminate details of their skeletal anatomy

Evolutionary timescale and genomic divergence for black basses. Our lab employs a cutting-edge genomics toolkit for interrogating species delimitation problems. From: https://doi.org/10.1038/s41598-022-11743-2

Phylogenomic species delimitation reduces recognized species diversity in the Antarctic plunderfishes (Pogonophryne) from 29 to six species. From: https://doi.org/10.1093/sysbio/syab057

Etheostoma xanthovum, an extraordinarily pigmented new species of darter, described by our lab in 2023. From: https://doi.org/10.3374/014.064.0102

Erosion creates patches of suitable habitat facilitating dispersal-mediated allopatric speciation in darters, illuminating a mechanism resulting in microendemic geographic distributions in the Mobile Basin. From: https://doi.org/10.1093/evolut/qpad156

Our lab uses different approaches to determine non-tree-like evolutionary histories, including repeated episodes of introgression, in species complexes like the Longear Sunfish (Lepomis megalotis). From: https://doi.org/10.1093/sysbio/syab029

The Sawfin Shiner, a species known for over five decades but never described, is being given a name by our lab.

Chromosome-level genome assemblies and demographic modeling show how speciation after migration into a lake is associated with a major structural change to the genome in darters. From: https://academic.oup.com/evolut/article/77/7/1505/7140304

Systematics based on molecular phylogenetics and morphology reconciles alternative classifications of Stripetail darters. From: https://doi.org/10.1643/i2021053

Identification of hidden bowfin species diversity. (a) Map of eastern North America showing museum specimen collection records of Amia calva (blue), Amia ocellicauda (yellow) and undetermined (tan), retrieved from fishnet2.net. Stars indicate type localities. Diamonds indicate specimens sampled in the ddRAD phylogenetic analysis. (b) Phylogeny and genomic structure analysis of 177 specimens of Amia based on 56 247 ddRAD loci. Photograph of A. ocellicauda from lower Tennessee River, Marshall County, Alabama, USA, YPM 035200, by J.M.M. and Amia calva from the Suwanee River, Gilchrist County, Florida, USA, UF 238466, by Z. Randall. (c) The comparison of pairwise Fst values for comparisons within A. calva (blue) and A. ocellicauda (yellow), and the comparisons between A. calva and A. ocellicauda (green). (d) Boxplot showing IO robusticity (ratio between maximum dorsoventral depth and maximum anteroposterior length) in A. calva and A. ocellicauda. CT-scanned skull of A. calva, TU 22613; CT-scanned skull of A. ocellicauda, TU 118772. DOI: 0.1098/rsbl.2022.0395

Photographs of live adult males of Etheostoma spilotum and E. sagitta, showing individual variation in color and pigment pattern. Etheostoma spilotum: A. Nuptial condition, 72 mm SL, Clemons Fork, Breathitt County, Kentucky, 21 May 2007, INHS 167434. B. Nuptial condition, 74 mm SL, Big Double Creek, Clay County, Kentucky, 23 April 2007, INHS 128086. C. Non-nuptial condition, 65 mm SL, Hell Creek, Lee County, Kentucky, 18 May 2007, INHS 167435. Etheostoma sagitta: D. Nuptial condition, 69 mm SL, Cogur Fork, McCreary County, Kentucky, 14 April 2021, photographed and released. E. Nuptial condition, 62 mm SL, Sweet Gum Branch, McCreary County, Kentucky, 27 April 2007, INHS uncataloged. F. Non-nuptial condition, 82 mm TL, Barren Fork, McCreary County, 1 June 2006, photographed and released. Scale bar equals 1 cm. Abbreviations: SL, standard length; TL, total length. Photographs by M.R. Thomas. DOI: 10.3374/014.064.0103