Specimen collection is essential for modern science.

Natural history museums are vital repositories of specimens, samples and data that inform about the natural world; this Formal Comment revisits a Perspective that advocated for the adoption of compassionate collection practices, querying whether it will ever be possible to completely do away with whole animal specimen collection.

Gene loss and relaxed selection of plaat1 in vertebrates adapted to low-light environments.

Gene loss is an important mechanism for evolution in low-light or cave environments where visual adaptations often involve a reduction or loss of eyesight. The plaat gene family are phospholipases essential for the degradation of organelles in the lens of the eye. They translocate to damaged organelle membranes, inducing them to rupture. This rupture is required for lens transparency and is essential for developing a functioning eye. Plaat3 is thought to be responsible for this role in mammals, while plaat1 is thought to be responsible in other vertebrates. We used a macroevolutionary approach and comparative genomics to examine the origin, loss, synteny, and selection of plaat1 across bony fishes and tetrapods. We show that plaat1 (likely ancestral to all bony fish + tetrapods) has been lost in squamates and is significantly degraded in lineages of low-visual acuity and blind mammals and fish. Our findings suggest that plaat1 is important for visual acuity across bony vertebrates, and that its loss through relaxed selection and pseudogenization may have played a role in the repeated evolution of visual systems in low-light-environments. Our study sheds light on the importance of gene-loss in trait evolution and provides insights into the mechanisms underlying visual acuity in low-light environments.

The complete mitochondrial genome of the Mexican blind brotula Typhlias pearsei (Ophidiiformes: Dinematichthydae): an endemic and troglomorphic cavefish from the Yucatán Peninsula karst aquifer.

In this study we report the first complete and annotated mitochondrial genome of the Mexican blind brotula, Typhlias pearsei, a troglobitic cavefish endemic to the Yucatán peninsula karst aquifer in southeastern Mexico. Genomic sequencing was accomplished via next generation sequencing (NGS). The resulting mitogenome is 16,813 bp long and, as in most vertebrates, consists of a total of 37 genes (13 PCGs, 2 rRNAs, 22 tRNAs) and two non-coding regions (control region and origin of the light strand replication). Other than a rearrangement in the position of two tRNAs (shuffling between tRNA-Ile and tRNA-Gln), the mitogenome of T. pearsei exhibits a genomic composition and organization similar to that of most teleost mitogenomes. Besides offering this valuable genomic resource for future studies, the resulting mitogenome was used in a comparative context to test the current higher-level taxonomy of ophidiiform fishes and to examine the phylogenetic position of T. pearsei among viviparous brotulas. Our phylogenetic results confirm those from the most comprehensive molecular phylogenetic study of the group.

The complete mitochondrial genome of the Mexican-endemic cavefish Ophisternoninfernale (Synbranchiformes, Synbranchidae): insights on patterns of selection and implications for synbranchiform phylogenetics.

Ophisternoninfernale is one of the 200+ troglobitic fish species worldwide, and one of the two cave-dwelling fishes endemic to the karstic aquifer of the Yucatán Peninsula, Mexico. Because of its elusive nature and the relative inaccessibility of its habitat, there is virtually no genetic information on this enigmatic fish. Herein we report the complete mitochondrial genome of O.infernale, which overall exhibits a configuration comparable to that of other synbranchiforms as well as of more distantly related teleosts. The KA/KS ratio indicates that most mtDNA PCGs in synbranchiforms have evolved under strong purifying selection, preventing major structural and functional protein changes. The few instances of PCGs under positive selection might be related to adaptation to decreased oxygen availability. Phylogenetic analysis of mtDNA comparative data from synbranchiforms and closely related taxa (including the indostomid Indostomusparadoxus) corroborate the notion that indostomids are more closely related to synbranchiforms than to gasterosteoids, but without rendering the former paraphyletic. Our phylogenetic results also suggest that New World species of Ophisternon might be more closely related to Synbranchus than to the remaining Ophisternon species. This novel phylogenetic hypothesis, however, should be further tested in the context of a comprehensive systematic study of the group.

Accelerated Diversification Explains the Exceptional Species Richness of Tropical Characoid Fishes.

The Neotropics harbor the most species-rich freshwater fish fauna on the planet, but the timing of that exceptional diversification remains unclear. Did the Neotropics accumulate species steadily throughout their long history, or attain their remarkable diversity recently? Biologists have long debated the relative support for these museum and cradle hypotheses, but few phylogenies of megadiverse tropical clades have included sufficient taxa to distinguish between them. We used 1288 ultraconserved element loci spanning 293 species, 211 genera, and 21 families of characoid fishes to reconstruct a new, fossil-calibrated phylogeny and infer the most likely diversification scenario for a clade that includes a third of Neotropical fish diversity. This phylogeny implies paraphyly of the traditional delimitation of Characiformes because it resolves the largely Neotropical Characoidei as the sister lineage of Siluriformes (catfishes), rather than the African Citharinodei. Time-calibrated phylogenies indicate an ancient origin of major characoid lineages and reveal a much more recent emergence of most characoid species. Diversification rate analyses infer increased speciation and decreased extinction rates during the Oligocene at around 30 Ma during a period of mega-wetland formation in the proto-Orinoco-Amazonas. Three species-rich and ecomorphologically diverse lineages (Anostomidae, Serrasalmidae, and Characidae) that originated more than 60 Ma in the Paleocene experienced particularly notable bursts of Oligocene diversification and now account collectively for 68% of the approximately 2150 species of Characoidei. In addition to paleogeographic changes, we discuss potential accelerants of diversification in these three lineages. While the Neotropics accumulated a museum of ecomorphologically diverse characoid lineages long ago, this geologically dynamic region also cradled a much more recent birth of remarkable species-level diversity. [Biodiversity; Characiformes; macroevolution; Neotropics; phylogenomics; ultraconserved elements.].

Cave-dwelling populations of Rhamdia (Siluriformes: Heptapteridae) from the Sierra de Zongolica, Veracruz, Mexico: an evidence-based checklist with comments on their evolutionary history and taxonomy.

In this study, the authors present a comprehensive checklist of cave-dwelling populations of Rhamdia from the Sierra de Zongolica (SdZ) in Veracruz, Mexico, including two new records, based on permanent and verifiable evidence in the form of voucher specimens. The authors use phylogenetic and phylogeographic analyses of voucher-derived comparative cytochrome b data to shed light on the evolutionary history of these populations. The results of this study, while preliminary, suggest that hypogean forms of Rhamdia from the SdZ are cave-adapted populations of the more widespread and epigean species R. laticauda.

Resting-state EEG alpha/theta ratio related to neuropsychological test performance in Parkinson's Disease.

OBJECTIVE: To determine possible associations of hemispheric-regional alpha/theta ratio (α/θ) with neuropsychological test performance in Parkinson's Disease (PD) non-demented patients. METHODS: 36 PD were matched to 36 Healthy Controls (HC). The α/θ in eight hemispheric regions was computed from the relative power spectral density of the resting-state quantitative electroencephalogram (qEEG). Correlations between α/θ and performance in several neuropsychological tests were conducted, significant findings were included in a moderation analysis. RESULTS: The α/θ in all regions was lower in PD than in HC, with larger effect sizes in the posterior regions. Right parietal, and right and left occipital α/θ had significant positive correlations with performance in Judgement of Line Orientation Test (JLOT) in PD. Adjusted moderation analysis indicated that right, but not left, occipital α/θ influenced the JLOT performance related to PD. CONCLUSIONS: Reduction of the occipital α/θ, in particular on the right side, was associated with visuospatial performance impairment in PD. SIGNIFICANCE: Visuospatial impairment in PD, which is highly correlated with the subsequent development of dementia, is reflected in α/θ in the right posterior regions. The right occipital α/θ may represent a useful qEEG marker for evaluating the presence of early signs of cognitive decline in PD and the subsequent risk of dementia.

Pattern and timing of diversification in the African freshwater fish genus Distichodus (Characiformes: Distichodontidae).

BACKGROUND: Distichodus is a clade of tropical freshwater fishes currently comprising 25 named species distributed continent-wide throughout the Nilo-Sudan and most Sub-Saharan drainages. This study investigates the phylogenetic relationships, timing of diversification, and biogeographic history of the genus from a taxonomically comprehensive mutilocus dataset analyzed using Maximum Likelihood and Bayesian methods of phylogenetic inference, coalescence-based species-tree estimation, divergence time estimation, and inference of geographic range evolution. RESULTS: Analyses of comparative DNA sequence data in a phylogenetic context reveal the existence of two major clades of similar species-level diversity and provide support for the monophyletic status of most sampled species. Biogeographic reconstruction on a time-scaled phylogeny suggest that the origins of the genus date back to the late Oligocene and that current geographic distributions are the result of a Congo Basin origin followed by dispersal and range expansion into adjacent ichthyofaunal provinces at different times during the evolutionary history of the group. CONCLUSIONS: We present the most comprehensive phylogenetic, chronological, and biogeographic treatment yet conducted for the genus. The few instances of species paraphyly (D. teugelsi, D. fasciolatus) revealed by the resulting phylogenies are likely a consequence of post-divergence introgressive hybridization and/or incomplete lineage sorting due to recent speciation. Historical biogeographic findings are both in agreement and conflict with previous studies of other continent-wide African freshwater fish genera, suggesting a complex scenario for the assemblage of Africa's continental ichthyofaunal communities.

DNA barcoding uncovers extensive cryptic diversity in the African long-fin tetra Bryconalestes longipinnis (Alestidae: Characiformes).

To investigate the presence of cryptic diversity in the African longfin-tetra Bryconalestes longipinnis, we employed DNA barcoding in a phylogeographic context, as well as geometric morphometrics, documenting for the first time genetic and body shape variation in the species. Analysis of cytochrome oxidase I gene (coI) sequence variation exposed extremely high levels of genetic differentiation among samples from across the geographic range of the species (up to 18%), certainly much greater than the traditionally employed c. 3% sequence divergence heuristic threshold for conspecifics. Phylogeographic analyses of coI data revealed eight clusters/clades that diverge by >4% and up to 18% (p-distance), potentially representing cryptic members of a species complex. A clear biogeographic pattern was also uncovered, in which the two main coI lineages corresponded geographically with the upper Guinea (UG) and lower Guinea (LG) ichthyofaunal provinces of continental Africa, respectively. Within each of these main lineages, however, no apparent phylogeographic structuring was found. Despite strong genetic differentiation, there is considerable overlap in body shape variation between UG and LG populations. For the most part, morphological variation does not match the strength of the molecular phylogeographic signal. Therefore, the ability to reliably utilise external body shape for regional delimitation remains elusive. Further anatomical investigation appears necessary to establish whether compelling diagnostic morphological features do exist between the divergent lineages of the B. longipinnis complex uncovered in this study.

Phylogenomic Systematics of Ostariophysan Fishes: Ultraconserved Elements Support the Surprising Non-Monophyly of Characiformes.

Ostariophysi is a superorder of bony fishes including more than 10,300 species in 1100 genera and 70 families. This superorder is traditionally divided into five major groups (orders): Gonorynchiformes (milkfishes and sandfishes), Cypriniformes (carps and minnows), Characiformes (tetras and their allies), Siluriformes (catfishes), and Gymnotiformes (electric knifefishes). Unambiguous resolution of the relationships among these lineages remains elusive, with previous molecular and morphological analyses failing to produce a consensus phylogeny. In this study, we use over 350 ultraconserved element (UCEs) loci comprising 5 million base pairs collected across 35 representative ostariophysan species to compile one of the most data-rich phylogenies of fishes to date. We use these data to infer higher level (interordinal) relationships among ostariophysan fishes, focusing on the monophyly of the Characiformes-one of the most contentiously debated groups in fish systematics. As with most previous molecular studies, we recover a non-monophyletic Characiformes with the two monophyletic suborders, Citharinoidei and Characoidei, more closely related to other ostariophysan clades than to each other. We also explore incongruence between results from different UCE data sets, issues of orthology, and the use of morphological characters in combination with our molecular data. [Conserved sequence; ichthyology; massively parallel sequencing; morphology; next-generation sequencing; UCEs.].

A new species of Ptychochromis from southeastern Madagascar (Teleostei: Cichlidae).

We describe a new species in the endemic Malagasy cichlid genus Ptychochromis. Ptychochromis mainty, new species, is known from four individuals, all collected in the Fort Dauphin region of southeastern Madagascar, and shares a palatine morphology (eastern-type palatine) with other eastern congeners. Ptychochromis mainty is distinguished from all congeners by a nearly uniform dark brown to black pigmentation pattern in preservation and by the presence of a relatively continuous and expansive black longitudinal midlateral blotch in life, extending from the posterior margin of the opercle to the caudal peduncle. The new species is further distinguished from other eastern Ptychochromis species by having minimal or no overlap of the first supraneural with the dorsoposterior region of the supraoccipital crest (vs. marked overlap). We present a molecular-based phylogeny for all available Ptychochromis species, which supports the hypothesis that P. mainty is a distinct taxon. The new species is recovered as the sister taxon to P. grandidieri within a clade comprising species with an eastern-type palatine morphology. We present a geometric morphometric analysis that provides additional evidence to distinguish P. mainty from congeners.

DNA barcoding reveals novel insights into pterygophagy and prey selection in distichodontid fishes (Characiformes: Distichodontidae).

DNA barcoding was used to investigate dietary habits and prey selection in members of the African-endemic family Distichodontidae noteworthy for displaying highly specialized ectoparasitic fin-eating behaviors (pterygophagy). Fin fragments recovered from the stomachs of representatives of three putatively pterygophagous distichodontid genera (Phago, Eugnathichthys, and Ichthyborus) were sequenced for the mitochondrial gene co1. DNA barcodes (co1 sequences) were then used to identify prey items in order to determine whether pterygophagous distichodontids are opportunistic generalists or strict specialists with regard to prey selection and, whether as previously proposed, aggressive mimicry is used as a strategy for successful pterygophagy. Our findings do not support the hypothesis of aggressive mimicry suggesting instead that, despite the possession of highly specialized trophic anatomies, fin-eating distichodontids are opportunistic generalists, preying on fishes from a wide phylogenetic spectrum and to the extent of engaging in cannibalism. This study demonstrates how DNA barcoding can be used to shed light on evolutionary and ecological aspects of highly specialized ectoparasitic fin-eating behaviors by enabling the identification of prey species from small pieces of fins found in fish stomachs.

Are characiform fishes Gondwanan in origin? Insights from a time-scaled molecular phylogeny of the Citharinoidei (Ostariophysi: Characiformes).

Fishes of the order Characiformes are a diverse and economically important teleost clade whose extant members are found exclusively in African and Neotropical freshwaters. Although their transatlantic distribution has been primarily attributed to the Early Cretaceous fragmentation of western Gondwana, vicariance has not been tested with temporal information beyond that contained in their fragmentary fossil record and a recent time-scaled phylogeny focused on the African family Alestidae. Because members of the suborder Citharinoidei constitute the sister lineage to the entire remaining Afro-Neotropical characiform radiation, we inferred a time-calibrated molecular phylogeny of citharinoids using a popular Bayesian approach to molecular dating in order to assess the adequacy of current vicariance hypotheses and shed light on the early biogeographic history of characiform fishes. Given that the only comprehensive phylogenetic treatment of the Citharinoidei has been a morphology-based analysis published over three decades ago, the present study also provided an opportunity to further investigate citharinoid relationships and update the evolutionary framework that has laid the foundations for the current classification of the group. The inferred chronogram is robust to changes in calibration priors and suggests that the origins of citharinoids date back to the Turonian (ca 90 Ma) of the Late Cretaceous. Most modern citharinoid genera, however, appear to have originated and diversified much more recently, mainly during the Miocene. By reconciling molecular-clock- with fossil-based estimates for the origins of the Characiformes, our results provide further support for the hypothesis that attributes the disjunct distribution of the order to the opening of the South Atlantic Ocean. The striking overlap in tempo of diversification and biogeographic patterns between citharinoids and the African-endemic family Alestidae suggests that their evolutionary histories could have been strongly and similarly influenced by Miocene geotectonic events that modified the landscape and produced the drainage pattern of Central Africa seen today.

Phylogenetic relationships and the temporal context for the diversification of African characins of the family Alestidae (Ostariophysi: Characiformes): evidence from DNA sequence data.

Phylogenetic relationships within the family Alestidae were investigated using parsimony, maximum likelihood, and Bayesian approaches based on a molecular dataset that included both nuclear and mitochondrial markers. Multiple representatives of all but two of the recognized alestid genera were included, which allowed for testing previous hypotheses of intergeneric relationships and the monophyly of several genera. The phylogenetic position of the Neotropical genus Chalceus with respect to the family Alestidae was also examined. In order to understand the temporal context of alestid diversification, Bayesian methods of divergence time estimation using fossil data in the form of calibration priors were used to date the nodes of the phylogenetic tree. Our results rejected the monophyly of the family as currently recognized (Alestidae sensu lato) and revealed several instances of poly- and paraphyly among genera. The genus Chalceus was recovered well nested within Neotropical characiforms, thus rejecting the hypothesis that this taxon is the most basal alestid. The estimated mean divergence time for the alestid clade (Alestidae sensu stricto) was 54 Mya with a 95% credibility interval of 63-49 Mya. These results are incongruent with the hypothesis that the origin of the family Alestidae predates the African-South American Drift-Vicariance event.