Alan R. Lemmon’s research while affiliated with Florida State University and other places

Color polymorphism, the occurrence of multiple discrete color morphs with co-adapted sets of traits within the same population, may provide the raw materials for rapid species formation. It has been hypothesized that fixation of a single morph can result in character release, whereby the monomorphic form evolves without the constraint of accommodating multiple adaptive peaks. However, the rates of evolution between populations fixed for different morphs likely depend on the specific adaptive zones occupied by each morph. We studied the evolution of dorsal color polymorphism (striped and unstriped morphs) in woodland salamanders ( Plethodon ), a North American radiation in which the polymorphism can be found in even the most distantly related species (~44 Ma divergence). We estimated a phylogenomic tree of Plethodon , representing all extant taxa with multiple samples for most species. Morphometric data suggest that between-species variation exists predominantly along an axis of relative body elongation, likely corresponding to a terrestrial–fossorial continuum. Polymorphic species occupy an intermediate phenotypic space between the evolutionary optima of striped and unstriped species, although polymorphic species did not have elevated speciation rates. Faster rates of body shape evolution were observed in unstriped species, suggesting that body elongation, which is co-adapted with the unstriped morph, is constrained by the polymorphism. Striped species had slower rates of evolution than polymorphic species, despite lacking the genetic constraints often associated with polymorphism. Our results demonstrate that rates of phenotypic evolution and speciation following character release can be asymmetric and idiosyncratic depending on the alternative adaptations of each morph.

Although biologists have described biofluorescence in a diversity of taxa, there have been few systematic efforts to document the extent of biofluorescence within a taxonomic group or investigate its general significance. Through a field survey across South America, we discover and document patterns of biofluorescence in tropical amphibians. We more than triple the number of anuran species that have been tested for this trait. We find evidence for ecological tuning (i.e., the specific adaptation of a signal to the environment in which it is received) of the biofluorescent signals. For 56.58% of species tested, the fluorescence excitation peak matches the wavelengths most abundant at twilight, the light environment in which most frogs are active. Additionally, biofluorescence emission spans both wavelengths of low availability in twilight and the peak sensitivity of green-sensitive rods in the anuran eye, likely increasing contrast of this signal for a conspecific receiver. We propose an expanded key for testing the ecological significance of biofluorescence in future studies, providing potential explanations for the other half of fluorescent signals not originally meeting formerly proposed criteria. With evidence of tuning to the ecology and sensory systems of frogs, our results suggest frog biofluorescence is likely functioning in anuran communication.

In vicariant species formation, divergence results primarily from periods of allopatry and restricted gene flow. Widespread species harboring differentiated, geographically distinct sublineages offer a window into what may be a common mode of species formation, whereby a species originates, spreads across the landscape, then fragments into multiple units. However, incipient lineages usually lack reproductive barriers that prevent their fusion upon secondary contact, blurring the boundaries between a single, large metapopulation-level lineage and multiple independent species. Here we explore this model of species formation in the Eastern Red-backed Salamander (Plethodon cinereus), a widespread terrestrial vertebrate with at least six divergent mitochondrial clades throughout its range. Using anchored hybrid enrichment data, we applied phylogenomic and population genomic approaches to investigate patterns of divergence, gene flow, and secondary contact. Genomic data broadly match most mitochondrial groups but reveal mitochondrial introgression and extensive admixture at several contact zones. While species delimitation analyses in BPP supported five lineages of P. cinereus, genealogical divergence indices (gdi) were highly sensitive to the inclusion of admixed samples and the geographic representation of candidate species, with increasing support for multiple species when removing admixed samples or limiting sampling to a single locality per group. An analysis of morphometric data revealed differences in body size and limb proportions among groups, with a reduction of forelimb length among warmer and drier localities consistent with increased fossoriality. We conclude that P. cinereus is a single species, but one with highly structured component lineages of various degrees of independence.

Abstract: Species are the fundamental unit of biodiversity studies. However, many species complexes are difficult to delimit, especially those characterized by complicated patterns of population structure. Salamanders in the family Plethodontidae often form species by slowly fragmenting across a landscape over space and time. They thus provide many examples of species complexes in which gradual Darwinian evolution has resulted in multiple units of varying degrees of differentiation, including incompletely separated lineages. Herein, we report on a molecular systematic investigation of woodland salamanders in the Plethodon wehrlei group, a group that has recently been split from two species into five species. To quantify patterns of genetic variation, we collected genetic samples from 24 individuals from 20 populations, including all species and representing a carefully selected subset of previous work. From these samples, we obtained genomic data by using anchored hybrid enrichment, resulting in 319 loci averaging 1300 bp in length. Biallelic single-nucleotide polymorphisms were randomly selected from 316 of these loci for some analyses. We examined patterns of genetic structure by using a combination of multivariate statistics and methods based on evolutionary models (such as the Bayesian program STRUCTURE) and found that all of the recognized species formed genetic clusters; however, P. wehrlei and P. punctatus were relatively weakly differentiated and STRUCTURE identified three separate clusters within P. jacksoni. Species trees inferred using the weighted accurate species tree algorithm (wASTRAL), Bayesian phylogenetics and phylogeography (BPP), and TreeMix all recovered the same topology, with P. dixi sister to the other taxa, which included a northern clade (P. wehrlei, P. punctatus, P. pauleyi) and a southern clade (P. jacksoni, with three separate groups). TreeMix only inferred one gene flow event. We evaluated the candidate species by using BPP and the genealogical divergence index (gdi). Although BPP delimited all candidate species with strong support (all posterior probabilities = 1.0), the gdi only strongly supported P. dixi and P. pauleyi, both of which have only been recently described. We discuss the difficult problem of species delimitation in groups that form species via range fragmentation. We also provide a vision for future research, with the aim of better testing and diagnosing the species diversity within the P. wehrlei group.

Recent molecular taxonomic advancements have expanded our understanding of crocodylian diversity, revealing the existence of previously overlooked species, including the Congo dwarf crocodile (Osteolaemus osborni) in the central Congo Basin rainforests. This study explores the genomic divergence between O. osborni and its better-known relative, the true dwarf crocodile (Osteolaemus tetraspis), shedding light on their evolutionary history. Field research conducted in the northwestern Republic of the Congo uncovered a locality where both species coexist in sympatry/syntopy. Genomic analysis of sympatric individuals reveals a level of divergence comparable to that between ecologically similar South American dwarf caimans (Paleosuchus palpebrosus and Paleosuchus trigonatus), suggesting parallel speciation in the Afrotropics and Neotropics during the Middle to Late Miocene, 10–12 Ma. Comparison of the sympatric and allopatric dwarf crocodiles indicates no gene flow between the analysed sympatric individuals of O. osborni and O. tetraspis. However, a larger sample will be required to answer the question of whether or to what extent these species hybridize. This study emphasizes the need for further research on the biology and conservation status of the Congo dwarf crocodile, highlighting its significance in the unique biodiversity of the Congolian rainforests and thus its potential as a flagship species.

A comprehensive phylogeny of north European Geometridae is reconstructed using a two‐step analytical pipeline. First, a phylogenomic backbone tree was inferred using a 117‐species subset of geometrid moths and a 35‐species set of outgroup taxa from eight other macroheteroceran families. The data matrix totalled 209,499 bp from 648 protein‐coding loci obtained using anchored hybrid enrichment technique for sequencing. This backbone was used for constructing a larger phylogeny of Geometridae based on up to 11 ‘traditional’ protein‐coding genes which were obtained for all 376 species of north European geometrids, complemented by 98 species from taxonomic key groups of Geometridae from other parts of the world. Our results largely corroborate earlier findings about higher classification of Geometridae, but new evidence nevertheless allows us to suggest several changes to the taxonomy. Lampropterygini Õunap & Nedumpally tribus nova and Pelurgini Õunap & Nedumpally tribus nova (both Larentiinae) are described. Epirranthini are regarded as a junior subjective synonym of Rumiini syn. n. Triphosini and Macariini are shown to be paraphyletic within their current limits. Costaconvexa Agenjo is transferred from Xanthorhoini to Epirrhoini new tribe association , Artiora Meyrick from Ennomini incertae sedis to Boarmiini new tribe association , Selenia Hübner from Ennominae incertae sedis to Epionini new tribe association and Epirranthis Hübner from Epirranthini to Rumiini new tribe association . Ochyria Hübner stat. rev. is revived from synonym of Xanthorhoe Hübner as a valid genus and Epelis Hulst stat. rev. and Speranza Curtis stat. rev. from synonyms of Macaria Curtis as valid genera, leading to the following new or revised combinations: Ochyria quadrifasiata (Clerck) rev. comb. , Epelis carbonaria (Clerck) comb. n. , Speranza fusca (Thunberg) comb. n. , Speranza artesiaria (Denis & Schiffermüller) rev. comb. , Speranza brunneata (Thunberg) rev. comb. , Speranza wauaria (Linnaeus) rev. comb. , Speranza loricaria (Eversmann) rev. comb. Perizoma saxicola Tikhonov rev. comb. is transferred back to its original genus from Gagitodes Warren. Hydrelia Hübner, Xanthorhoe and Heliomata Grote & Robinson are shown to be paraphyletic within their current limits.

ABSTRACT: The Cumberland Plateau Salamander, Plethodon kentucki, is a cryptic species with respect to the sympatric Northern Slimy Salamander, Plethodon glutinosus. It was first described by Highton and MacGregor (1983) by using allozyme data. In that description, the authors reported extreme levels of genetic differentiation for a single species with a narrow distribution; however, follow-up studies found patterns of genetic variation that were discordant with the allozyme data. In this paper, we describe patterns of genetic variation within P. kentucki by using an anchored hybrid enrichment dataset of 21 individuals sampled from across its known range. We identified four genetic groups with extensive admixture and isolation by distance. We constructed a population tree by using TreeMix and inferred gene flow between two of the four genetic groups. Finally, we used Bayesian phylogenetics and phylogeography (BPP) in conjunction with the genealogical divergence index (gdi) to test species boundaries within P. kentucki. Although BPP suggested that P. kentucki could be four species, gdi indicated that none of the groups were sufficiently independent to constitute separate species. We conclude that P. kentucki is best recognized as a single species with substantial genetic structure within its limited distribution.

We used nuclear genomic data and statistical models to evaluate the ecological and evolutionary processes shaping spatial variation in species richness in Calochortus (Liliaceae, 74 spp.). Calochortus occupies diverse habitats in the western United States and Mexico and has a center of diversity in the California Floristic Province, marked by multiple orogenies, winter rainfall, and highly divergent climates and substrates (including serpentine). We used sequences of 294 low-copy nuclear loci to produce a time-calibrated phylogeny, estimate historical biogeography, and test hypotheses regarding drivers of present-day spatial patterns in species number. Speciation and species coexistence require reproductive isolation and ecological divergence, so we examined the roles of chromosome number, environmental heterogeneity, and migration in shaping local species richness. Six major clades—inhabiting different geographic/climatic areas, and often marked by different base chromosome numbers (n = 6 to 10)—began diverging from each other ~10.3 Mya. As predicted, local species number increased significantly with local heterogeneity in chromosome number, elevation, soil characteristics, and serpentine presence. Species richness is greatest in the Transverse/Peninsular Ranges where clades with different chromosome numbers overlap, topographic complexity provides diverse conditions over short distances, and several physiographic provinces meet allowing immigration by several clades. Recently diverged sister-species pairs generally have peri-patric distributions, and maximum geographic overlap between species increases over the first million years since divergence, suggesting that chromosomal evolution, genetic divergence leading to gametic isolation or hybrid inviability/sterility, and/or ecological divergence over small spatial scales may permit species co-occurrence.

Caddisflies (Trichoptera) are among the most diverse groups of freshwater animals, with more than 16,000 described species. They play an outsized role in freshwater ecology and environmental engineering in streams, rivers, and lakes. Because of this, they are frequently used as indicator organisms in biomonitoring programs. Despite their importance, key questions concerning the evolutionary history of caddisflies, such as the timing and origin of larval case-making, have been unanswered due to the lack of a well-resolved phylogenetic tree. To shed light on these questions in Trichoptera, we estimated a phylogenetic tree using a combination of transcriptomes and targeted enrichment data for 206 species, representing 48 of 52 extant families and 174 genera. We calibrated and dated the tree with a set of 33 carefully selected fossils. The first caddisflies originated in the Permian, and the major suborders began to diversify in the Triassic. Ancestral state reconstruction and diversification analysis revealed that portable case-making evolved in three separate lineages, and shifts in diversification occurred in concert with key evolutionary innovations other than case-making.