2022
Chan W-P, Childers RR, Ashe S, Tsai C-C, Elson C, Keleher KJ, Sipe RLHawkins, Maier CA, Sourakov A, Gall LF, et al. A high-throughput multispectral imaging system for museum specimens. Nature Communications Biology. 2022;5 (1318).
Publisher's Version s42003-022-04282-z.pdf Talavera G, Lukhtanov V, Pierce NE, Vila R.
DNA Barcodes Combined with Multilocus Data of Representative Taxa Can Generate Reliable Higher-Level Phylogenies Bond J. Systematic Biology. 2022;71 (2) :382–395.
Publisher's VersionAbstractAbstract Taxa are frequently labeled incertae sedis when their placement is debated at ranks above the species level, such as their subgeneric, generic, or subtribal placement. This is a pervasive problem in groups with complex systematics due to difficulties in identifying suitable synapomorphies. In this study, we propose combining DNA barcodes with a multilocus backbone phylogeny in order to assign taxa to genus or other higher-level categories. This sampling strategy generates molecular matrices containing large amounts of missing data that are not distributed randomly: barcodes are sampled for all representatives, and additional markers are sampled only for a small percentage. We investigate the effects of the degree and randomness of missing data on phylogenetic accuracy using simulations for up to 100 markers in 1000-tips trees, as well as a real case: the subtribe Polyommatina (Lepidoptera: Lycaenidae), a large group including numerous species with unresolved taxonomy. Our simulation tests show that when a strategic and representative selection of species for higher-level categories has been made for multigene sequencing (approximately one per simulated genus), the addition of this multigene backbone DNA data for as few as 5–10% of the specimens in the total data set can produce high-quality phylogenies, comparable to those resulting from 100% multigene sampling. In contrast, trees based exclusively on barcodes performed poorly. This approach was applied to a 1365-specimen data set of Polyommatina (including ca. 80% of described species), with nearly 8% of representative species included in the multigene backbone and the remaining 92% included only by mitochondrial COI barcodes, a phylogeny was generated that highlighted potential misplacements, unrecognized major clades, and placement for incertae sedis taxa. We use this information to make systematic rearrangements within Polyommatina, and to describe two new genera. Finally, we propose a systematic workflow to assess higher-level taxonomy in hyperdiverse groups. This research identifies an additional, enhanced value of DNA barcodes for improvements in higher-level systematics using large data sets. [Birabiro; DNA barcoding; incertae sedis; Kipepeo; Lycaenidae; missing data; phylogenomic; phylogeny; Polyommatina; supermatrix; systematics; taxonomy]
talavera_barcode_2022.pdf Pierce NE, Dankowicz E.
The Natural History of Caterpillar-Ant Associations. In:
Marquis RJ, Koptur S Caterpillars in the Middle. Cham: Springer International Publishing ; 2022. pp. 319–391.
Publisher's VersionAbstractAbstract The caterpillars of many Lepidoptera are neither attacked nor tended by ants but nevertheless appear to be obligately ant-associated and benefit from the enemy-free space created by ants. Obligate myrmecophiles that do not attract ants through stridulatory or chemical signaling are limited to habitats where ants are reliably present for other reasons, either among ant-attended hemipterans, on ant-plants, or around ant nests. Particularly in the tropics, obligate ant associates that passively coexist with ants are more diverse than previously recognized, including, for example, hundreds of African species in the lycaenid subfamily Poritiinae. Mutualists and parasites of ants have been reported in eleven families: Tineidae, Tortricidae, Cyclotornidae, Coleophoridae, Crambidae, Erebidae, Notodontidae, Hesperiidae, Pieridae, Lycaenidae, and Riodinidae. Altogether, myrmecophily has originated at least 30 times in Lepidoptera, and many groups may remain undiscovered. The butterfly families Lycaenidae and Riodinidae contain the vast majority of ant-associated species: larvae of at least 3841 (71%) of the \textasciitilde5390 described Lycaenidae and 308 (20%) of the \textasciitilde1562 described Riodinidae are known or inferred to be ant-associated, and both families possess specialized, convergently developed exocrine glands and stridulatory devices to communicate with ants. Many caterpillar-ant relationships previously characterized as mutualisms may actually be parasitic, as caterpillars can manipulate ants and ultimately exert a fitness cost. In the family Lycaenidae, highly specialized and obligate ant associations are found largely in the Old World tropics, Australia, and Southern Africa, where the stoichiometry of soil micronutrients, particularly sodium and phosphorus, climate, host plants, and geography may all selectively shape caterpillar-ant associations.
pierce_dankowicz_book_chapter.pdf Ji Y, Baker CCM, Popescu VD, Wang J, Wu C, Wang Z, Li Y, Wang L, Hua C, Yang Z, et al. Measuring protected-area effectiveness using vertebrate distributions from leech iDNA. Nature Communications. 2022;13 (1) :1555.
Publisher's VersionAbstractAbstract Protected areas are key to meeting biodiversity conservation goals, but direct measures of effectiveness have proven difficult to obtain. We address this challenge by using environmental DNA from leech-ingested bloodmeals to estimate spatially-resolved vertebrate occupancies across the 677 km 2 Ailaoshan reserve in Yunnan, China. From 30,468 leeches collected by 163 park rangers across 172 patrol areas, we identify 86 vertebrate species, including amphibians, mammals, birds and squamates. Multi-species occupancy modelling shows that species richness increases with elevation and distance to reserve edge. Most large mammals (e.g. sambar, black bear, serow, tufted deer) follow this pattern; the exceptions are the three domestic mammal species (cows, sheep, goats) and muntjak deer, which are more common at lower elevations. Vertebrate occupancies are a direct measure of conservation outcomes that can help guide protected-area management and improve the contributions that protected areas make towards global biodiversity goals. Here, we show the feasibility of using invertebrate-derived DNA to estimate spatially-resolved vertebrate occupancies across entire protected areas.
baker_leech_idna_2022.pdf Wang Z, Li Y, Jain A, Pierce NE.
Agent-based models reveal limits of mark-release-recapture estimates for the rare butterfly, Bhutanitis thaidina (Lepidoptera: Papilionidae). Insect Sci. 2022;29 (2) :550-566.
AbstractInsect diversity and abundance are in drastic decline worldwide, but quantifying insect populations to better conserve them is a difficult task. Mark-release-recapture (MRR) is widely used as an ecological indicator for insect populations, but the accuracy of MRR estimates can vary with factors such as spatial scale, sampling effort and models of inference. We conducted a 3-year MRR study of B. thaidina in Yanzigou valley, Mt. Gongga but failed to obtain sufficient data for a robust population estimate. This prompted us to integrate B. thaidina life history information to parameterize agent-based models and evaluate the conditions under which successful MRR studies could be conducted. We evaluated: (1) the performance of MRR models under different landscape types, and (2) the influence of experimental design on the accuracy and variance of MRR-based estimates. Our simulations revealed systematic underestimates of true population parameters by MRR models when sampling effort was insufficient. In a total of 2772 simulations, subjective decisions in sampling protocol (e.g., frequency, number of sampling locations, use of spatially explicit models, type of estimands) accounted for nearly half of the variation in estimates. We conclude that MRR-based estimates could be improved with the addition of more field-specific parameters.
wang_bhutanitis_2022.pdf Bittleston LS, Benson EL, Bernardin JR, Pierce NE.
Characterization and Comparison of Convergence Among Cephalotus follicularis Pitcher Plant-Associated Communities With Those of Nepenthes and Sarracenia Found Worldwide. Front Plant Sci. 2022;13 :887635.
AbstractThe Albany pitcher plant, Cephalotus follicularis, has evolved cup-shaped leaves and a carnivorous habit completely independently from other lineages of pitcher plants. It is the only species in the family Cephalotaceae and is restricted to a small region of Western Australia. Here, we used metabarcoding to characterize the bacterial and eukaryotic communities living in C. follicularis pitchers at two different sites. Bacterial and eukaryotic communities were correlated in both richness and composition; however, the factors associated with richness were not the same across bacteria and eukaryotes, with bacterial richness differing with fluid color, and eukaryotic richness differing with the concentration of DNA extracted from the fluid, a measure roughly related to biomass. For turnover in composition, the variation in both bacterial and eukaryotic communities primarily differed with fluid acidity, fluid color, and sampling site. We compared C. follicularis-associated community diversity with that of Australian Nepenthes mirabilis, as well as a global comparison of Southeast Asian Nepenthes and North American Sarracenia. Our results showed similarity in richness with communities from other pitcher plants, and specific bacterial taxa shared among all three independent lineages of pitcher plants. Overall, we saw convergence in richness and particular clades colonizing pitcher plants around the world, suggesting that these highly specialized habitats select for certain numbers and types of inhabitants.
bittleston_cephalotus_2022.pdf Moreau CS, Pierce NE.
Edward O. Wilson (1929-2021). Nat Ecol Evol. 2022;6 (3) :240-241.
moreau_wilson_obit_2022.pdf Rabideau-Childers R, Angier KIW, Dean BZM, Blumstein M, Darling WS, Kennedy-Yoon A, Ziemke CH, Perez-Martinez CA, Wu D, Ye W, et al. Evidence of nutrient translocation in response to smoke exposure by the East African ant acacia, Vachellia drepanolobium. Ecol Evol. 2022;12 (1) :e8244.
AbstractFire is a major selective force on arid grassland communities, favoring traits such as the smoke-induced seed germination response seen in a wide variety of plant species. However, little is known about the relevance of smoke as a cue for plants beyond the seedling stage.We exposed a fire-adapted savanna tree, Vachellia (=Acacia) drepanolobium, to smoke and compared nutrient concentrations in leaf and root tissues to unexposed controls. Experiments were performed on three age cohorts: 2-year-old, 9-month-old, and 3-month-old plants.For the 2-year-old plants exposed to smoke, carbon and nitrogen concentrations were lower in the leaves and higher in the roots than controls. Less pronounced trends were found for boron and magnesium.In contrast, smoke-exposed 3-month-old plants had lower root nitrogen concentrations than controls. No significant differences were found in the 9-month-old plants, and no significant shifts in other nutrient concentrations were observed between plant tissues for any of the three age cohorts. Synthesis: Our findings are consistent with smoke-induced translocation of nutrients from leaves to roots in 2-year-old V. drepanolobium. This could represent a novel form of fire adaptation, with variation over the course of plant development. The translocation differences between age cohorts highlight the need to investigate smoke response in older plants of other species. Accounting for this adaptation could better inform our understanding of savanna community structure and nutrient flows under fire regimes altered by anthropogenic land use and climate change.
childers_vachellia_smoke_2022.pdf Wang Z, Pierce NE.
Fine-scale genome-wide signature of Pleistocene glaciation in Thitarodes moths (Lepidoptera: Hepialidae), host of Ophiocordyceps fungus in the Hengduan Mountains. Mol Ecol. 2022.
AbstractThe Hengduan Mountains region is a biodiversity hotspot known for its topologically complex, deep valleys and high mountains. While landscape and glacial refugia have been evoked to explain patterns of interspecies divergence, the accumulation of intra-species (i.e., population level) genetic divergence across the mountain-valley landscape in this region has received less attention. We used genome-wide restriction site-associated DNA sequencing (RADseq) to reveal signatures of Pleistocene glaciation in populations of Thitarodes shambalaensis (Lepidoptera: Hepialidae), the host moth of parasitic Ophiocordyceps sinensis (Hypocreales: Ophiocordycipitaceae) or "caterpillar fungus" endemic to the glacier of eastern Mt. Gongga. We used moraine history along the glacier valleys to model the distribution and environmental barriers to gene flow across populations of T. shambalaensis. We found that moth populations separated by less than 10 km exhibited valley-based population genetic clustering and isolation-by-distance (IBD), while gene flow among populations was best explained by models using information about their distributions at the local last glacial maximum (LGML , 58 kya), not their contemporary distribution. Maximum likelihood lineage history among populations, and among subpopulations as little as 500 m apart, recapitulated glaciation history across the landscape. We also found signals of isolated population expansion following the retreat of LGML glaciers. These results reveal the fine-scale, long-term historical influence of landscape and glaciation on the genetic structuring of populations of an endangered and economically important insect species. Similar mechanisms, given enough time and continued isolation, could explain the contribution of glacier refugia to the generation of species diversity among the Hengduan Mountains.
wang_thitarodes_2022.pdf Wang Z, Da W, Negi CS, Ghimire PL, Wangdi K, Yadav PK, Pubu Z, Lama L, Yarpel K, Maunsell SC, et al. Profiling, monitoring and conserving caterpillar fungus in the Himalayan region using anchored hybrid enrichment markers. Proc Biol Sci. 2022;289 (1973) :20212650.
AbstractThe collection of caterpillar fungus accounts for 50-70% of the household income of thousands of Himalayan communities and has an estimated market value of $5-11 billion across Asia. However, Himalayan collectors are at multiple economic disadvantages compared with collectors on the Tibetan Plateau because their product is not legally recognized. Using a customized hybrid-enrichment probe set and market-grade caterpillar fungus (with samples up to 30 years old) from 94 production zones across Asia, we uncovered clear geography-based signatures of historical dispersal and significant isolation-by-distance among caterpillar fungus hosts. This high-throughput approach can readily distinguish samples from major production zones with definitive geographical resolution, especially for samples from the Himalayan region that form monophyletic clades in our analysis. Based on these results, we propose a two-step procedure to help local communities authenticate their produce and improve this multi-national trade-route without creating opportunities for illegal exports and other forms of economic exploitation. We argue that policymakers and conservation practitioners must encourage the fair trade of caterpillar fungus in addition to sustainable harvesting to support a trans-boundary conservation effort that is much needed for this natural commodity in the Himalayan region.
wang_fungus_himalayan_2022.pdf 2021
Lienard MA, Bernard GD, Allen A, Lassance J-M, Song S, Childers RR, Yu N, Ye D, Stephenson A, Valencia-Montoya WA, et al. The evolution of red color vision is linked to coordinated rhodopsin tuning in lycaenid butterflies. PNAS. 2021;118 (6).
Salzman S, Crook D, Calonje M, Stevenson DW, Pierce NE, Hopkins R.
Cycad-Weevil Pollination Symbiosis Is Characterized by Rapidly Evolving and Highly Specific Plant-Insect Chemical Communication. Frontiers in Plant Science. 2021;12 :639368.
Publisher's VersionAbstractCoevolution between plants and insects is thought to be responsible for generating biodiversity. Extensive research has focused largely on antagonistic herbivorous relationships, but mutualistic pollination systems also likely contribute to diversification. Here we describe an example of chemically-mediated mutualistic species interactions affecting trait evolution and lineage diversification. We show that volatile compounds produced by closely related species of Zamia cycads are more strikingly different from each other than are other phenotypic characters, and that two distantly related pollinating weevil species have specialized responses only to volatiles from their specific host Zamia species. Plant transcriptomes show that approximately a fifth of genes related to volatile production are evolving under positive selection, but we find no differences in the relative proportion of genes under positive selection in different categories. The importance of phenotypic divergence coupled with chemical communication for the maintenance of this obligate mutualism highlights chemical signaling as a key mechanism of coevolution between cycads and their weevil pollinators.
salzman_cycad_weevil_2021.pdf Grewe F, Kronforst MR, Pierce NE, Moreau CS.
Museum genomics reveals the Xerces blue butterfly (Glaucopsyche xerces) was a distinct species driven to extinction. Biology Letters. 2021;17 (7) :20210123.
Publisher's VersionAbstractThe last Xerces blue butterfly was seen in the early 1940s, and its extinction is credited to human urban development. This butterfly has become a North American icon for insect conservation, but some have questioned whether it was truly a distinct species, or simply an isolated population of another living species. To address this question, we leveraged next-generation sequencing using a 93-year-old museum specimen. We applied a genome skimming strategy that aimed for the organellar genome and high-copy fractions of the nuclear genome by a shallow sequencing approach. From these data, we were able to recover over 200 million nucleotides, which assembled into several phylogenetically informative markers and the near-complete mitochondrial genome. From our phylogenetic analyses and haplotype network analysis we conclude that the Xerces blue butterfly was a distinct species driven to extinction.
grewe_xerces_2021.pdf Valencia-Montoya WA, Quental TB, Tonini JFR, Talavera G, Crall JD, Lamas G, Busby RC, Carvalho APS, Morais AB, Oliveira Mega N, et al. Evolutionary trade-offs between male secondary sexual traits revealed by a phylogeny of the hyperdiverse tribe Eumaeini (Lepidoptera: Lycaenidae). Proc Biol Sci. 2021;288 (1950) :20202512.
AbstractMale butterflies in the hyperdiverse tribe Eumaeini possess an unusually complex and diverse repertoire of secondary sexual characteristics involved in pheromone production and dissemination. Maintaining multiple sexually selected traits is likely to be metabolically costly, potentially resulting in trade-offs in the evolution of male signals. However, a phylogenetic framework to test hypotheses regarding the evolution and maintenance of male sexual traits in Eumaeini has been lacking. Here, we infer a comprehensive, time-calibrated phylogeny from 379 loci for 187 species representing 91% of the 87 described genera. Eumaeini is a monophyletic group that originated in the late Oligocene and underwent rapid radiation in the Neotropics. We examined specimens of 818 of the 1096 described species (75%) and found that secondary sexual traits are present in males of 91% of the surveyed species. Scent pads and scent patches on the wings and brush organs associated with the genitalia were probably present in the common ancestor of Eumaeini and are widespread throughout the tribe. Brush organs and scent pads are negatively correlated across the phylogeny, exhibiting a trade-off in which lineages with brush organs are unlikely to regain scent pads and vice versa. In contrast, scent patches seem to facilitate the evolution of scent pads, although they are readily lost once scent pads have evolved. Our results illustrate the complex interplay between natural and sexual selection in the origin and maintenance of multiple male secondary sexual characteristics and highlight the potential role of sexual selection spurring diversification in this lineage.
rspb.2020.2512.pdf Lienard MA, Bernard GD, Allen A, Lassance J-M, Song S, Childers RR, Yu N, Ye D, Stephenson A, Valencia-Montoya WA, et al. The evolution of red color vision is linked to coordinated rhodopsin tuning in lycaenid butterflies. PNAS. 2021;118 (6).
lienard_rhodopsin.pdf