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opencc-zeroDec 2020View details →

Delimitation despite discordance: Evaluating the species limits of a confounding species complex in the face of mitonuclear discordance

The delimitation of species is an essential pursuit of biology, and proper taxonomies are crucial for the assessment and conservation management of organismal diversity. However, delimiting species can be hindered by a number of factors including highly conserved morphologies (e.g. cryptic species), differences in criteria of species concepts, and discordance between gene topologies (e.g. mitonuclear discordance). Here we use a taxonomically confounded species complex of toads in Central America that exhibits extensive mitonuclear discordance to test delimitation hypotheses. Our investigation integrates mitochondrial sequences, nuclear SNPs, morphology, and macroecological data to determine which taxonomy best explains the divergence and evolutionary relationships among these toads. We found that a three species taxonomy following the distributions of the nuclear SNP haplotypes offer the best explanation of the species in this complex based off of the integrated data types. Due to the taxonomic instability of this group we also discuss conservation concerns in the face of improper taxonomic delimitation. Our study provides an empirical hypothesis testing framework to assess species delimitation hypotheses in the face of cryptic morphology and mitonuclear discordance and highlights the importance that proper taxonomy has over conservation related actions.

opencc-zeroDec 2017View details →

Data from: Artificial light at night confounds broad-scale habitat use by migrating birds

With many of the world's migratory bird populations in alarming decline, broad-scale assessments of responses to migratory hazards may prove crucial to successful conservation efforts. Most birds migrate at night through increasingly light-polluted skies. Bright light sources can attract airborne migrants and lead to collisions with structures, but might also influence selection of migratory stopover habitat and thereby acquisition of food resources. We demonstrate, using multi-year weather radar measurements of nocturnal migrants across the northeastern U.S., that autumnal migrant stopover density increased at regional scales with proximity to the brightest areas, but decreased within a few kilometers of brightly-lit sources. This finding implies broad-scale attraction to artificial light while airborne, impeding selection for extensive forest habitat. Given that high-quality stopover habitat is critical to successful migration, and hindrances during migration can decrease fitness, artificial lights present a potentially heightened conservation concern for migratory bird populations.

opencc-zeroDec 2014View details →

Data from: Model misspecification confounds the estimation of rates and exaggerates their time dependency

While welcoming the comment of Ho et al. (2015), we find little that undermines the strength of our criticism, and it would appear they have misunderstood our central argument. Here we respond with the purpose of reiterating that we are (i) generally critical of much of the evidence presented in support of the time-dependent molecular rate (TDMR) hypothesis and (ii) specifically critical of estimates of μ derived from tip-dated sequences that exaggerate the importance of purifying selection as an explanation for TDMR over extended timescales. In response to assertions put forward by Ho et al. (2015), we use panmictic coalescent simulations of temporal data to explore a fundamental assumption for tip-dated tree shape and associated mutation rate estimates, and the appropriateness and utility of the date randomization test. The results reveal problems for the joint estimation of tree topology, effective population size and μ with tip-dated sequences using beast. Given the simulations, beast consistently obtains incorrect topological tree structures that are consistent with the substantial overestimation of μ and underestimation of effective population size. Data generated from lower effective population sizes were less likely to fail the date randomization test yet still resulted in substantially upwardly biased estimates of rates, bringing previous estimates of μ from temporally sampled DNA sequences into question. We find that our general criticisms of both the hypothesis of time-dependent molecular evolution and Bayesian methods to estimate μ from temporally sampled DNA sequences are further reinforced.

opencc-zeroDec 2017View details →

Data from: Landscape history confounds the ability of the NDVI to detect fine-scale variation in grassland communities

1. The NDVI is a remotely-sensed vegetation index that is frequently used in ecological studies. There is, however, a lack of studies that evaluate the ability of the NDVI to detect fine-scale variation in grassland plant community composition and species richness. Ellenberg indicators characterize the environmental preferences of plant species – and community-mean Ellenberg values have been used to explore the environmental drivers of community assembly. 2. We used variation partitioning to test the ability of satellite-based NDVI to explain community-mean Ellenberg nutrient (mN) and moisture (mF) indices, and the richness of habitat-specialist species in dry grasslands of different ages. The grasslands represent a gradient of decreasing soil nutrient status. 3. If community composition is determined by the responses of individual species to the underlying environmental conditions and if, at the same time, community composition determines the optical characteristics of the vegetation canopy, then positive relationships between the NDVI and mN and mF are expected. Many grassland specialists are intolerant of nutrient-rich soils. If specialist richness is negatively related to soil-nutrient levels, then a negative association between the NDVI and specialist richness is expected. However, because grassland community composition is not only influenced by abiotic variables but also by other spatial and temporal drivers, we included spatial variables and grassland age in the statistical analyses. 4. The NDVI explained the majority of the variation in mF, and also contributed to a substantial proportion of the variation in mN. However, variation in specialist richness and the lowest values of mN were explained by grassland age and spatial variables – but were poorly explained by the NDVI. 5. Synthesis and applications. The NDVI showed a good ability to detect variation in plant community composition, and should provide a valuable tool for assessing fine-scale environmental variation in grasslands or for monitoring changes in grassland habitat properties. However, because the concentration of grassland specialists not only depends on environmental variables but also on the age and spatial context of the grasslands, the NDVI is unlikely to allow the identification of grasslands with high numbers of specialist species.

opencc-zeroMar 2022View details →

Data from: Historical mitochondrial genome introgression confounds species delimitation—evidence from phylogenetic inference in the Odorrana grahami species complex

Species delimitation is essential to informing conservation policy and understanding ecological and evolutionary processes. Most of our recent gains in knowledge on animal diversity rely on morphological characteristics and mitochondrial (mt) DNA variation. Concordant results based on both have led to an unprecedented acceleration in the identification of new species and enriched the field of taxonomy. However, discordances are also found commonly between morphological and mtDNA evidence. This confounds species delimitation, especially when gene flow or mitochondrial genome introgression has occurred. Here we illustrate how mitochondrial genome introgression among species of the Odorrana grahami complex confounds species delimitation using the combined evidence of morphological characters, mitochondrial variation, and thousands of nuclear single nucleotide polymorphisms (SNPs) from genotyping-by-sequencing (GBS). Fifty-eight samples across the distribution of the O. grahami complex were included. The mtDNA matrilineal genealogy indicated two clades, with O. grahami and O. junlianensis clustered together. In contrast, all nuclear evidence including gene trees, species trees, and genetic structure analyses based on GBS data support three species with distinct genetic clusters. These three distinct genetic clusters also correspond to distinct morphological characters. They affirm the distinct taxonomic entities of both O. grahami and O. junlianensis, as well as a third clade distinct from either. Which species the third clade belongs to remains unclear and will require further testing. The nuclear genomic loci contradict the COI evidence, with indications of rampant historical mitochondrial genome introgression among the species of the O. grahami complex. These discordant signals previously confused species delimitation efforts in this group. Based on these findings, we recommend the integration of independent data, especially nuclear genomic evidence, in species delimitation so as to be robust against the pitfalls of mitochondrial introgression.

opencc-zeroJun 2022View details →

Methodological confounds of measuring urinary oxidative stress in wild animals

Biomarkers of oxidative stress (OS) are useful in addressing a wide range of research questions, but thus far, they have had limited application to wild mammal populations due to a reliance on blood or tissue sampling. A shift towards non-invasive measurement of OS would allow field ecologists and conservationists to apply this method more readily. However, the impact of methodological confounds on urinary OS measurement under field conditions has never been explicitly investigated. We combined a cross-sectional analysis with a field experiment to assess the impact of four potential methodological confounds on OS measurements: 1) time of sampling, 2) environmental contamination from foliage; 3) delay between sample collection and flash-freezing in liquid nitrogen; 4) sample storage of up to 15 months below -80C. We measured DNA oxidative damage (8-hydroxy-2'-deoxyguanosine, 8-OHdG), lipid peroxidation (malondialdehyde, MDA), Total Antioxidant Capacity (TAC) and uric acid (UA) in 167 urine samples collected from wild Zanzibar red colobus (Piliocolobus kirkii). We found that MDA was higher in samples collected in the morning than in the afternoon but there were no diurnal patterns in any of the other markers. Contamination of samples from leaf surfaces and time frozen at -80°C for up to 15 months did not affect OS marker concentrations. Freezing delay did not affect OS levels cross-sectionally, but OS values from individual samples showed only moderate to good consistency and substantial rank order reversals when exposed to different freezing delays. We recommend that the impact of storage time on OS marker concentrations and diurnal patterns of OS markers be considered when designing sampling protocols. However, given the high stability we observed for four OS markers subject to a variety of putative methodological confounds, we suggest that urinary OS markers provide a valuable addition to the toolkit of field ecologists and conservationists within reasonable methodological constraints.

Figure 10. a in A new Callichirus ghost shrimp species from the southwestern Atlantic, long confounded with C. major (Say, 1818) (Decapoda: Axiidea: Callichiridae)

Figure 10. a, Callichirus aff. major Colombia, male major cheliped dactylus and fixed finger, lateral view, USNM 266225; b, Callichirus corruptus sp. nov., male major cheliped dactylus and fixed finger, lateral view, MZUSP 41251; c, Callichirus corruptus sp. nov., female major cheliped merus, lateral view, MZUSP 41252; d, Callichirus garthi, male major cheliped ischium, lateral view, MUAP-CD 0432–2011; e, Callichirus garthi, sixth pleomere, uropods and telson, dorsal view, MUAP-CD 0432–2011; f, Callichirus islagrande, male major cheliped merus and ischium (courtesy of Nuno Simões), lateral view; g, Callichirus adamas, male major cheliped merus and ischium (modified from Kensley 1974), lateral view; h, Callichirus islagrande, sixth pleomere, uropods and telson, dorsal view, USNM 69362. Scale bars: 10 mm.

Figure 7. Callichirus major. a, b in A new Callichirus ghost shrimp species from the southwestern Atlantic, long confounded with C. major (Say, 1818) (Decapoda: Axiidea: Callichiridae)

Figure 7. Callichirus major. a, b, neotype, male (cl 13.2 mm), Indian River, Florida, USA, USNM 228086. c, e, male (cl: 20.6 mm), New River, North Carolina, USA, USNM 266227. d, male (cl: 24.4 mm), Louisiana, Gulf Of Mexico, USA, USNM 79171. f, female (cl: 16.3 mm), Indian River, Florida, USA, USNM 228087. a, carapace front, eyestalks, and antennular and antennal peduncles, dorsal view; b, male major cheliped claw, lateral view; c, d, male second pleopod, external surface; e, male major cheliped claw, lateral view; f, female major cheliped, lateral view. Scale bars: a = 2 mm; b, e, f = 1 cm; c, d = 1 mm.

Figure 6 in A new Callichirus ghost shrimp species from the southwestern Atlantic, long confounded with C. major (Say, 1818) (Decapoda: Axiidea: Callichiridae)

Figure 6. Molecular phylogenetic tree represented as maximum likelihood topology of the partial mitochondrial DNA sequence of the 16S rDNA gene to place Callichirus corruptus sp. nov. Nodal support values represent the frequencies observed using 1000 bootstrap pseudo-replicates. Values below 50% are not represented.

Figure 4 in A new Callichirus ghost shrimp species from the southwestern Atlantic, long confounded with C. major (Say, 1818) (Decapoda: Axiidea: Callichiridae)

Figure 4. Callichirus corruptus sp. nov.; holotype, male (cl: 18.8 mm), MZUSP 41251. a–d, second, third, fourth and fifth pereopods, respectively, lateral view. Scale bars: 2 mm.

Figure 2 in A new Callichirus ghost shrimp species from the southwestern Atlantic, long confounded with C. major (Say, 1818) (Decapoda: Axiidea: Callichiridae)

Figure 2. Callichirus corruptus sp. nov. a–d, holotype, male (cl: 18.8 mm), MZUSP 41251; e, paratype, male (cl: 18.6 mm), MZUSP 41253. a, body, lateral view; b, carapace and cephalic appendages, lateral view (arrows indicate branchiostegal lobe and emargination on central part of carapace); c, anterior part of carapace and cephalic appendages, dorsal view; d, basal part of antennal peduncle, dorsal view (setae omitted; arrow indicates scaphocerite); e, right third maxilliped, external surface. Scale bars: a = 1 cm; b, c = 2 mm; d = 1 mm; e = 4 mm.

Figure 1. a in A new Callichirus ghost shrimp species from the southwestern Atlantic, long confounded with C. major (Say, 1818) (Decapoda: Axiidea: Callichiridae)

Figure 1. a, male and female specimen of Callichirus corruptus sp. nov. from the Brazilian coast (MZUSP 39027); b, collection sites (empty circles) for Callichirus corruptus sp. nov. along the Brazilian coast. Scale bar: A = 1 cm.

Figure 9. Male pleopod 2 in A new Callichirus ghost shrimp species from the southwestern Atlantic, long confounded with C. major (Say, 1818) (Decapoda: Axiidea: Callichiridae)

Figure 9. Male pleopod 2 and third maxilliped, external surface. a, Callichirus adamas (modified from Kensley 1974); b, Callichirus corruptus sp. nov., MZUSP 41251; c, Callichirus islagrande, USNM 69362; d, Callichirus major, USNM 228086; e, Callichirus santarosaensis (modified from Sakai and Türkay 2012); f, Callichirus adamas (modified from Kensley 1974); g, Callichirus garthi, MZUC-UCCC 7311; h, Callichirus seilacheri, MZUCR 3335–01. Scale bars: a–d = 1 mm; e–h = 5 mm.

Figure 3 in A new Callichirus ghost shrimp species from the southwestern Atlantic, long confounded with C. major (Say, 1818) (Decapoda: Axiidea: Callichiridae)

Figure 3. Callichirus corruptus sp. nov. a, c, holotype, male (cl: 18.8 mm), MZUSP 41251; b, d, paratype, female (cl: 20.4 mm), MZUSP 41252. a, c, male major and minor chelipeds, respectively, lateral view; b, d, female major and minor chelipeds, respectively, lateral view. Scale bars: 1 cm.

Figure 5 in A new Callichirus ghost shrimp species from the southwestern Atlantic, long confounded with C. major (Say, 1818) (Decapoda: Axiidea: Callichiridae)

Figure 5. Callichirus corruptus sp. nov. a, b, d, f, holotype, male (cl: 18.8 mm), MZUSP 41251; c, e, paratype, female (cl: 20.4 mm), MZUSP 41252. a, sixth pleomere, uropods and telson, dorsal view; b, c, male and female first pleopods, respectively, external surface; d, e, male and female second pleopods, respectively, external surface; f, third to fifth pleopods, external surface. Scale bars: a, c, e, f = 2 mm; b, d = 1 mm.

Figure 8 in A new Callichirus ghost shrimp species from the southwestern Atlantic, long confounded with C. major (Say, 1818) (Decapoda: Axiidea: Callichiridae)

Figure 8. Carapace and cephalic appendages, dorsal view. a, Callichirus corruptus sp. nov., MZUSP 41251; b, Callichirus garthi, MUAP-CD 0426/2011; c, Callichirus islagrande (courtesy of Nuno Simões); d, Callichirus major, USNM 228086; e, Callichirus santarosaensis (modified from Sakai and Türkay 2012); f, Callichirus seilacheri, MZUCR 3335–01. Scale bars: 10 mm.