Jeffrey Streicher

Natural History Museum, London · Department of Life Sciences

The processes that restrict gene flow between populations are fundamental to speciation. Here, we develop a simple framework for studying whether divergence in morphology, climatic niche, time and space contribute to reduced gene flow among populations and species. We apply this framework to a model system involving a clade of spiny lizards (Scelop...

Genomic architecture has played a key role in the evolution of biodiversity. Structural comparisons of genome sequences have informed the study of supergenes, sex chromosomes, and some of the earliest divergences in the tree of life. However, multi-species comparisons of whole genome sequences still have many computational and analytical limitation...

Non-visual opsins are transmembrane proteins expressed in the eyes and other tissues of many animals. When paired with a light-sensitive chromophore, non-visual opsins form photopigments involved in various non-visual, light-detection functions including circadian rhythm regulation, light-seeking behaviors, and seasonal responses. Here we investiga...

Visual systems adapt to different light environments through several avenues including optical changes to the eye and neurological changes in how light signals are processed and interpreted. Spectral sensitivity can evolve via changes to visual pigments housed in the retinal photoreceptors through gene duplication and loss, differential and coexpre...

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.

Large-scale, time-calibrated phylogenies from supermatrix studies have become crucial for evolutionary and ecological studies in many groups of organisms. However, in frogs (anuran amphibians), there is a serious problem with existing supermatrix estimates. Specifically, these trees are based on a limited number of loci (15 or fewer), and the highe...

Natural history specimens are a widely used and valuable resource for conservation, ecology, and evolutionary biology. One might assume that these collections are representative of natural populations, but recent work has suggested that many collections have disproportionately more male than female specimens. Here, we investigate sex ratios in > 5...

In the era of human-driven climate change, understanding whether behavioural buffering of temperature change is linked with organismal fitness is essential. According to the 'cost-benefit' model of thermoregulation, animals that live in environments with high frequencies of favourable thermal microclimates should incur lower thermoregulatory costs,...

Evolutionary shifts in chromosome compositions (karyotypes) are major drivers of lineage and genomic diversification. Fusion of ancestral chromosomes is one hypothesized mechanism for the evolutionary reduction of the total chromosome number; a frequently implied karyotypic shift. Empirical tests of this hypothesis require model systems with variab...

The data available for reconstructing molecular phylogenies have become wildly disparate. Phylogenomic studies can generate data for thousands of genetic markers for dozens of species, but for hundreds of other taxa, data may be available from only a few genes. Can these two types of data be integrated to combine the advantages of both, addressing...

Malagasy frogs of the subgenus Brygoomantis in the mantellid frog genus Mantidactylus currently comprise 14 described species of mostly brown, riparian frogs. Data from DNA barcoding suggested that the diversity of this subgenus is dramatically underestimated by current taxonomy. We here provide a comprehensive revision of this subgenus. We use hyb...

In numerous clades, divergent sister species have largely non-overlapping geographic ranges. This pattern presumably arises because species diverged in allopatry or parapatry, prior to a subsequent contact. Here, we provide population-genomic evidence for the opposite scenario: previously sympatric ecotypes that have spatially separated into diverg...

The shape and relative size of an ocular lens affect the focal length of the eye, with consequences for visual acuity and sensitivity. Lenses are typically spherical in aquatic animals with camera-type eyes and axially flattened in terrestrial species to facilitate vision in optical media with different refractive indices. Frogs and toads (Amphibia...

Non-visual opsins are transmembrane proteins expressed in the eyes, skin, and brain of many animals. When paired with a light-sensitive chromophore, non-visual opsins form photopigment systems involved in various non-visual, light-detection functions, including circadian rhythm regulation, light-seeking behavior, and detection of seasonality. Previ...

Pupil constriction has important functional consequences for animal vision, yet the evolutionary mechanisms underlying diverse pupil sizes and shapes are poorly understood. We aimed to quantify the diversity and evolution of pupil shapes among amphibians and to test for potential correlations to ecology based on functional hypotheses. Using photogr...

Snakes comprise nearly 4,000 extant species found on all major continents except Antarctica. Morphologically and ecologically diverse, they include burrowing, arboreal, and marine forms, feeding on prey ranging from insects to large mammals. Snakes are strikingly different from their closest lizard relatives, and their origins and early diversifica...

Seven species of the Asian torrent frogs (genus Amolops) have previously been reported from the eastern Himalayan country of Bhutan. Species identifications from the region have been largely based on photographed animals with few voucher specimens available and no molecular sampling. Understanding the taxonomic status of Bhutan’s torrent frogs has...

This article talks about the Amolops species in Bhutan and also describes new to science species from Bhutan.

Background Differences in morphology, ecology, and behavior through ontogeny can result in opposing selective pressures at different life stages. Most animals, however, transition through two or more distinct phenotypic phases, which is hypothesized to allow each life stage to adapt more freely to its ecological niche. How this applies to sensory s...

The spectral characteristics of vertebrate ocular lenses affect the image of the world that is projected onto the retina, and thus help shape diverse visual capabilities. Here, we tested whether amphibian lens transmission is driven by adaptation to diurnal activity (bright light) and/or scansorial habits (complex visual environments). Spectral tra...

Parapatric distributions between ecologically similar species have the potential to reveal the effects of limiting similarity in large-scale patterns of species coexistence. We present a qualitative model that predicts three different types of parapatric boundaries between competing species pairs: gap parapatry, abrupt parapatry and narrow sympatry...

Parapatric distributions between ecologically similar species have the potential to reveal the effects of limiting similarity in large-scale patterns of species coexistence. We present a qualitative model that predicts three different types of parapatric boundaries between competing species pairs: gap parapatry, abrupt parapatry and narrow sympatry...

Mantellid frogs of the Madagascar-endemic Gephyromantis plicifer complex consist of three nominal species (G. luteus, G. plicifer and G. sculpturatus) as well as several genetically divergent lineages (candidate species), but uncertainties surround the identity of the name-bearing types of all three established nomina. We applied laboratory techniq...

How will organisms cope when forced into warmer-than-preferred thermal environments? This is a key question facing our ability to monitor and manage biota as average annual temperatures increase, and is of particular concern for range-limited terrestrial species unable to track their preferred climatic envelope. Being ectothermic, desiccation prone...

Natricine snakes are geographically widespread, species rich (with ~250 extant species) and both morphologically and ecologically diverse. We present a multilocus DNA sequence phylogeny for 249 natricine specimens representing 189 named species, including 69 specimens and 21 species not previously sampled. Our inferred Bayesian and maximum likeliho...

We present a genome assembly from an individual female Rana temporaria (the common frog; Chordata; Amphibia; Anura; Ranidae). The genome sequence is 4.11 gigabases in span. The majority of the assembly is scaffolded into 13 chromosomal pseudomolecules. Gene annotation of this assembly by the NCBI Eukaryotic Genome Annotation Pipeline has identified...

We present a genome assembly from an individual male Bufo bufo (the common toad; Chordata; Amphibia; Anura; Bufonidae). The genome sequence is 5.04 gigabases in span. The majority of the assembly (99.1%) is scaffolded into 11 chromosomal pseudomolecules. Gene annotation of this assembly by the NCBI Eukaryotic Genome Annotation Pipeline has identifi...

Pupil constriction has important functional consequences for animal vision, yet the evolutionary mechanisms underlying diverse pupil sizes and shapes, often among animals that occupy optically similar environments, are poorly understood. We aimed to quantify the diversity and evolution of pupil shapes among amphibians and test for potential correla...

Terraranae is a large clade of New World direct-developing frogs that includes 3–5 families and >1,100 described species (∼15% of all named frog species). The relationships among major groups of terraranan frogs have been highly contentious, including conflicts among four recent phylogenomic studies utilizing 95, 220, 389, and 2,214 nuclear loci, r...

A correction to this paper has been published: https://doi.org/10.1007/s10682-021-10109-w

Whole mitochondrial genomes have been helpful in estimating phylogenetic relationships in many organismal groups, including caecilian amphibians. Despite the increasing ease of obtaining mitochondrial genome sequences from high-throughput sequencing, several species of caecilian lack this important molecular resource. As part of a targeted-sequence...

Intraspecific variation in colour pattern is widespread across multitudinous amphibian species. In some species, many distinct colour patterns are maintained within populations, a phenomenon referred to as exuberant colour polymorphism. The underlying causes of exuberant colour pattern polymorphism are poorly understood but are likely explained by...

Many animals have complex life cycles where larval and adult forms have distinct ecologies and habitats that impose different demands on their sensory systems. While the adaptive decoupling hypothesis predicts reduced genetic correlations between life stages, how sensory systems adapt across life stages at the molecular level is not well understood...

Animals with biphasic lifecycles often inhabit different visual environments across ontogeny. Many frogs and toads (Amphibia: Anura) have free-living aquatic larvae (tadpoles) that metamorphose into adults that inhabit a range of aquatic and terrestrial environments. Ecological differences influence eye size across species, but these relationships...

The genus Matoatoa includes two Malagasy endemic species, M. brevipes and M. spannringi. Due to their cryptic behaviour, the two species are known only from a handful of specimens and have been included in few molecular studies. Here we carried out a molecular barcoding analysis using a fragment of the mitochondrial NADH dehy-drogenase subunit 2 (N...

We describe two new species of salamanders of the genus Oedipina, subgenus Oe-dopinola, from two localities on the northwestern foothills of Ecuador, at elevations between 921 and 1,067 m. These are the southernmost members of the genus. We examined different museum collections and we found just three specimens of Oedipina from Ecuador, obtained th...

Frogs and toads (Amphibia: Anura) display diverse ecologies and behaviours, which are often correlated with visual capacity in other vertebrates. Additionally, anurans exhibit a broad range of relative eye sizes, which have not previously been linked to ecological factors in this group. We measured relative investment in eye size and corneal size f...

Metamorphosis is widespread across the animal kingdom and induces fundamental changes in the morphology, habitat and resources used by an organism during its lifetime. Metamorphic species are likely to experience more dynamic selective pressures through ontogeny compared with species with single-phase life cycles, which may drive divergent evolutio...

Discordance between the mitochondrial and nuclear genomes is a prevalent phenomenon in nature, in which the underlying processes responsible are considered to be important in shaping genetic variation in natural populations. Among the evolutionary processes that best explain such genomic mismatches incomplete lineage sorting and introgression are c...

The subgenus Mantidactylus is a group of frogs endemic to Madagascar, including the largest anuran species on the island. Although these frogs are common and widely distributed, their taxonomy remains unclear. Two species are currently recognised, M. grandidieri and M. guttulatus, with another available name, Rana pigra, considered to be a synonym...

We review morphology and systematics of Phoxophrys using new specimens of previously rare species. In addition to external characters, we relied heavily on skull morphology visualized using computed tomography data of all currently recognized species in this genus. Phylogenetic analysis of ND4, 12S, and 16S mDNA sequences reveal that Ph. tuberculat...

Narrow-mouthed frogs (Anura: Microhylidae) are globally distributed and molecular data suggest the rapid evolution of multiple subfamilies shortly after their origin. Despite recent progress, several subfamilial relationships remain unexplored using phylogenomic data. We analysed 1,796 nuclear ultraconserved elements, a total matrix of 400,664 nucl...

A comprehensive, accurate, and revisable alpha taxonomy is crucial for biodiversity studies, but is challenging when data from reference specimens are difficult to collect or observe. However, recent technological advances can overcome some of these challenges. To illustrate this, we used modern approaches to tackle a centuries-old taxonomic enigma...

Background: Terraranae is a large clade of New World direct-developing frogs that includes 3–5 families and >1,000 described species, encompassing ~15% of all named frog species. The relationships among major groups of terraranan frogs have been highly contentious, including conflicts among three recent phylogenomic studies utilizing 95, 389, and 2...

Since 1984 there have been no records of Rhaebo colomai (Hoogmoed, 1985) within the territory of Ecuador. This species was known from 2 localities in the province of Carchi, northwestern Ecuador, and the department of Nariño, southwestern Colombia, which were reported in 1979 and 2015, respectively. We report the recent sightings of R. colomai at 3...

BACKGROUND Aphytis melinus DeBach (Hymenoptera: Aphelinidae) is a highly effective biocontrol agent of the California red scale Aonidiella aurantii (Maskell) (Hemiptera: Diaspididae). It is commercially reared and used for augmentative releases within integrated pest management programs. However, mass rearing of biocontrol agents can result in popu...

Restriction site‐associated DNA sequencing (RADseq) has emerged as a useful tool in systematics and population genomics. A common feature of RADseq data sets is that they contain missing data that arise from multiple sources including genealogical sampling bias, assembly methodology and sequencing error. Many RADseq studies have demonstrated that a...

Introgression is now commonly reported in studies across the Tree of Life, aided by recent advancements in data collection and analysis. Nevertheless, researchers working with non‐model species lacking reference genomes may be stymied by a mismatch between available resources and methodological demands. In this study, we demonstrate a fast and simp...

Among New World direct-developing frogs belonging to the clade Brachycephaloidea (= Terraranae), there are several genera with uncertain phylogenetic placements. One notable example is the genus Niceforonia Goin & Cochran 1963, which includes three species that are endemic to Colombia. Three specimens of the species Niceforonia nana were collected...

Spatial and demographic expansion can alter patterns of genetic variation and have predictable spatial and temporal consequences. Two-dimensional range expansion should result in genetic variation that is correlated with the geographical axis of expansion. Notably, populations across the range of a geographically widespread species may experience e...

High‐throughput sequencing data have greatly improved our ability to understand the processes that contribute to current biodiversity patterns. The “vanishing refuge” diversification model is speculated for the coastal forests of eastern Africa, whereby some taxa have persisted and diversified between forest refugia, while others have switched to b...

We used Massively Parallel High-Throughput Sequencing to obtain genetic data from a 145-year old holotype specimen of the flying lizard, Draco cristatellus . Obtaining genetic data from this holotype was necessary to resolve an otherwise intractable taxonomic problem involving the status of this species relative to closely related sympatric Draco s...

ND2 sequence data for members of the Draco fimbriatus group plus 13 mitochondrial sequence reads obtained from the D. cristatellus holotype This file includes ND2 sequence data obtained via traditional Sanger sequencing for 39 individuals representing Draco cristatellus, D. fimbriatus, D. hennigi, D. punctatus, and D. maculatus, plus 183 base pairs...

We used Massively Parallel High-Throughput Sequencing to obtain genetic data from a 145-year old holotype specimen of the flying lizard, Draco cristatellus. Obtaining genetic data from this holotype was necessary to resolve an otherwise intractable taxonomic problem involving the status of this species relative to closely related sympatric Draco sp...

We describe two diminutive species of rattlesnakes (genus Crotalus) from small nearshore islands off the coast of Baja California in the western Gulf of California, Mexico. In order to test the hypothesis that some island populations represent cohesive species entities, we applied linear discriminant analysis and uniform validation procedures to mu...

Reduced representation genome sequencing has ushered in new methods for understanding how life evolved on earth. These methods utilise genetic data in the form of dozens, hundreds or even thousands of loci to estimate phylogenetic relationships. This approach, often termed phylogenomic analysis, has the potential to resolve controversial evolutiona...

We used Massively Parallel High-Throughput Sequencing to obtain genetic data from a 145-year old holotype specimen of the flying lizard, Draco cristatellus . Obtaining genetic data from this holotype was necessary to resolve an otherwise intractable taxonomic problem involving the status of this species relative to closely related sympatric Draco s...

Phylogenomic approaches offer a wealth of data, but a bewildering diversity of methodological choices. These choices can strongly affect the resulting topologies. Here, we explore two controversial approaches (binning genes into "supergenes" and inclusion of only rapidly evolving sites), using new data from hyloid frogs. Hyloid frogs encompass ∼53%...

Squamate reptiles (lizards and snakes) are the most diverse group of terrestrial vertebrates, with >10,000 species. Despite considerable effort to resolve relationships among major squamates clades, some branches have remained difficult. Among the most vexing has been the placement of snakes among lizard families, with most studies yielding only we...

Allopatric divergence following the formation of geographical features has been implicated as a major driver of evolutionary diversification. Widespread species complexes provide opportunities to examine allopatric divergence across varying degrees of isolation in both time and space. In North America, several geographical features may play such a...

Exceptional Specimens: The type series of the toad Bufo intermedius in 'Exceptional Specimens' edited and selected by B. H. Garner, in Evolve Magazine, the members' magazine of the Natural History Museum