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FIG. 2 in Hill forest dweller: a new cryptic species of Rhinolophus in the 'pusillus group' (Chiroptera: Rhinolophidae) from Thailand and Lao PDR
FIG. 2. Noseleaf (a–c) and dorsal (d) and ventral (e) pelage of R. monticolus sp. nov. PSUZC-MM2013.14 (paratype) from Thailand. Not to scale
FIGURE 4. Variation between H. calverti and H. americana females. Intersternite and S10 in Hetaerina calverti (Odonata: Zygoptera: Calopterygidae) sp. nov., a new cryptic species of the American Rubyspot complex
FIGURE 4. Variation between H. calverti and H. americana females. Intersternite and S10 of H. calverti (A) and H. americana (B). The illustrations are not at scale.
FIGURE 2 in Hetaerina calverti (Odonata: Zygoptera: Calopterygidae) sp. nov., a new cryptic species of the American Rubyspot complex
FIGURE 2. Paratype male of H. calverti (left) and young male of H. americana (right) from Apazapan, Veracruz, Mexico.
FIGURE 8 in A new cryptic species of fringe-toed lizards from southwestern Arizona with a revised taxonomy of the Uma notata species complex (Squamata: Phrynosomatidae)
FIGURE 8. (A) An individual of U. thurmanae in its natural habitat. (B) Sand dune habitat of U. thurmanae (camera pointed east with the Mohawk Dunes in the midground and the Mohawk Mountains in the background). Photographs by A. Gottscho.
FIGURE 6 in A new cryptic species of fringe-toed lizards from southwestern Arizona with a revised taxonomy of the Uma notata species complex (Squamata: Phrynosomatidae)
FIGURE 6. Holotype (USNM 590033) of Uma thurmanae showing (A) dorsal and (B) ventral head; (C) dorsal right hindfoot and (D) dorsal right forefoot showing toe fringes. Photographs by E. Langan and J. Poindexter.
FIGURE 7 in A new cryptic species of fringe-toed lizards from southwestern Arizona with a revised taxonomy of the Uma notata species complex (Squamata: Phrynosomatidae)
FIGURE 7. Satellite map of collecting localities for the type series of Uma thurmanae. Locations where specimens were collected, denoted by red stars, lie along the Mohawk Dunes, a long strip running northwest to southeast. The lizards are isolated in this dune system by the parallel Mohawk Mountains to the east, the Gila River and Interstate-8 to the north, and alluvial fans to the west and south, ultimately resulting in speciation. Source: "Mohawk Dunes," 32° 34' N, 113° 38' W, Google Earth. Imagery date: May 29, 2016. Accessed: July 3, 2018.
FIGURE 5 in A new cryptic species of fringe-toed lizards from southwestern Arizona with a revised taxonomy of the Uma notata species complex (Squamata: Phrynosomatidae)
FIGURE 5. (A) Dorsal and (B) ventral view of the adult female holotype (USNM 590033) of Uma thurmanae. Photographs by E. Langan and J. Poindexter.
FIGURE 3 in A new cryptic species of fringe-toed lizards from southwestern Arizona with a revised taxonomy of the Uma notata species complex (Squamata: Phrynosomatidae)
FIGURE 3. Box-and-whisker plots for discrete morphological characters that exhibited significant pairwise differences between OTUs. See Appendix 2 for details of how the characters were measured. SPLB=Supralabial Scales; SPCIL=Supraciliary Scales; INS=Internasal Scales; FP=Femoral Pores.
FIGURE 4 in A new cryptic species of fringe-toed lizards from southwestern Arizona with a revised taxonomy of the Uma notata species complex (Squamata: Phrynosomatidae)
FIGURE 4. Locations of Uma specimens in the morphospace defined by the first two axes of a Discriminant Function Analysis of morphological characters. Top: when specimens with broken tails are included and TL excluded (n=57), U. inornata can still be distinguished from other OTUs, but U. notata overlaps considerably with U. rufopunctata and U. cowlesi overlaps considerably with U. sp. Bottom: analysis of only the specimens with intact tails such that tail length (TL) could be measured (n=32) allows each OTU to be distinguished.
FIGURE 1 in A new cryptic species of fringe-toed lizards from southwestern Arizona with a revised taxonomy of the Uma notata species complex (Squamata: Phrynosomatidae)
FIGURE 1. Approximate geographic distributions of members of the U. notata species complex and its sister species, U. scoparia (adapted from Gottscho et al. 2017). Actual geographic distributions are more fragmented than shown by the shaded areas as the lizards are restricted to windblown sand habitats within those areas.
Data from: Between an ocean and a high place: coastal drainage isolation generates endemic cryptic species in the Cape Kurper Sandelia capensis (Anabantiformes: Anabantidae), Cape Region, South Africa
This study investigated the range-wide phylogenetics and biogeography of the Cape Kurper Sandelia capensis, a primary freshwater fish endemic to, and widespread within, the Cape Floristic Region (CFR) of South Africa. Maximum likelihood, Bayesian phylogenetic, and haplotype network analyses, based on two mitochondrial and two nuclear genes, revealed the existence of three reciprocally monophyletic, deeply divergent and allopatric clades that likely represent cryptic species. The West Coast Clade is largely confined to the Langvlei, Verlorenvlei, Berg, and Diep rivers, the Klein River Clade is endemic to the Klein River, and the South Coast Clade is found everywhere else in the range of S. capensis sensu lato. It was hypothesized that divergences within S. capensis sensu lato likely occurred because of (1) isolation of coastal drainages by persistent drainage divides and/or (2) vicariance of current tributaries by the drowning of their confluences by high sea levels. The current distribution of lineages could be due to historical range expansion and gene flow via (1) river capture or some other mode of transdivide dispersal, and/or (2) dispersal during periods of low sea level via paleoriver confluences of currently isolated coastal rivers. Comparison of BEAST2 estimated divergence times with the timing of climatic, geological, and geomorphological events supported long-term coastal drainage isolation, punctuated by rare transdivide dispersal events and limited paleoriver dispersal, as the best explanation of current phylogeographic and divergence patterns in S. capensis. Hydrological barriers that block upstream passage in palaeotributaries could hypothetically explain why S. capensis failed to disperse through certain palaeoriver confluences. There were several sites where biogeographic patterns have likely been confounded by human translocation of S. capensis. Alien fish predators and water extraction may threaten the three cryptic species more severely than previously realized, due to their smaller population sizes and inhabitation of only a portion of the range previously ascribed to S. capensis sensu lato. The preponderance of cryptic diversity and endemism in the CFR suggests that additional undescribed cryptic species of obligate freshwater fishes may be found in short coastal river systems around the world, especially in regions with a history of geological stability and a narrow continental shelf.
Data from: Cryptic phylogeographic history sheds light on the generation of species diversity in sky-island mountains
Biodiversity hotspots should be given high priority for conservation under the situation of global climate change. The sky islands in southwestern China are characterized by extraordinarily high species diversity and are among one of the world's top biodiversity hotspots. However, neither the actual species diversity in this region or mechanisms generating this diversity are well explored. Here, we report on the phylogeographic analysis of the long-tailed mole (Scaptonyx fusicaudus), a semi-fossorial mammal that inhabits the montane cool forests across the Chinese sky islands and is considered to represent one species divided into two subspecies. Analyses using DNA sequence data from one mitochondrial and six nuclear genes revealed that populations inhabiting different mountains exhibited exceptionally strong geographic structure. The lowlands and large rivers act as "soft" and "hard" barriers to dispersal, respectively, isolating evolutionary lineages for up to 11 million years. Our results suggest that the mountain ranges act as interglacial refugia buffering populations from climate fluctuations, further facilitating allopatric diversification. Strikingly, species delimitation analyses suggests that the long-tailed mole may comprise 18 operational taxonomic units and 17 putative species. Our results suggest that for low-vagility species, the complex topography of the Chinese sky islands has shaped genetic diversity and structure and promoted exceptional diversification through a combination of eco-environmental stability as well as geographic fragmentation. The patterns observed in S. fusicaudus may be representative for other cold-adapted species, reflecting the generation of mammalian faunal diversity in the sky-island mountains of southwestern China.
Data from: Wintering grounds, population size and evolutionary history of a cryptic passerine species from isotopic and genetic data
<p>Cryptic species pose a particular challenge to biologists in the context of life history investigations because of the difficulty in their field discrimination. Additionally, there is normally a lag in their widespread acceptance by the scientific community once they are formally recognised. These two factors might constrain our ability to properly assess the conservation status of the different species conforming a cryptic complex. In this study, we analysed isotopic and genetic data to shed light into the still unclear wintering grounds, population size and evolutionary history of the Iberian chiffchaff (<i>Phylloscopus ibericus</i>), a species included within the Common chiffchaff (<i>Phylloscopus collybita</i>) until two decades ago due to their phenotypic similarity. We used molecular methods to identify spring-migrating <i>Phylloscopus</i> species captured in northern Iberia, and by comparing the Hydrogen isotopic ratios of their claw tips (δ<sup>2</sup>H<sub>c</sub>; which would reflect the signatures of their wintering grounds), we detected that δ<sup>2</sup>H<sub>c</sub> values of Iberian chiffchaffs were similar to Willow warblers (<i>Phylloscopus trochilus</i>; a renowned trans-Saharan migrant), and higher than Common chiffchaffs (mostly a pre-Saharan migrant). These results strongly support the idea that Iberian chiffchaffs winter in tropical Africa. We additionally reconstructed the phylogeny and evolutionary history of the Iberian chiffchaff's clade using mitochondrial and nuclear markers. Our results revealed relatively high values of nucleotide diversity (and, hence, high N<sub>e</sub>) for the species that were greater than the values of the Common/Iberian most recent common ancestor. This suggests that the Iberian chiffchaff did not experience strong bottlenecks after diverging from the Common chiffchaff approximately one million years ago. Ultimately, our study provides another illustrative example of how isotopic and genetic analysis tools can help to enhance our understanding of avian ecology and evolution.</p>
Cryptic species and genetic connectivity among populations of the coral Pocillopora damicornis (Scleractinia) in the tropical southwestern Pacific
<p>Studying population genetic connectivity (i.e., identifying gene flow among populations and understanding their impacts on the genetic structure and diversity of populations) is first a matter of knowing what we work on, that is, accurately delimiting evolutionary units. Here, we focused on <em>Pocillopora damicornis</em> sensu stricto (or <em>Pocillopora </em>PSH04 sensu Gélin et al. in Mol Phylogenet Evol 109:430–446. http://dx.doi.org/10.1016/j.ympev.2017.01.018, 2017). From 458 colonies sampled within the tropical southwestern Pacific [Chesterfield Islands and New Caledonia (Grande Terre and Loyalty Islands)], Bayesian assignments and network analyses were conducted with 11-microsatellite loci to first evaluate the genetic partitioning of the colonies in distinct Secondary Species Hypotheses (SSHs), then in distinct clusters. Population genetic connectivity was then assessed for each cluster separately. <em>Pocillopora </em>PSH04 was partitioned into two highly differentiated SSHs (SSH04a and SSH04b), regularly found in sympatry. Furthermore, SSH04a was subdivided into two clusters (SSH04a-1 and SSH04a-2). This pattern of genetic structuring seems not related to clonality, but rather to the establishment of reproductive barriers. Nevertheless, considering each cluster separately, the populations appeared highly differentiated, suggesting relatively weak gene flow. This low connectivity among populations, coupled with the existence of cryptic species, brings new insights to the connectivity pattern of this understudied Pacific region.</p> <p>This dataset contains the microsatellite genotypes analysed (458 <em>Pocillopora</em> PSH04 colonies × 13 loci).</p>
Cryptic lineages respond differently to coral bleaching
<p>Coral cover is decreasing worldwide largely as a result of a rise in seawater temperatures that triggers coral bleaching and induces coral mortality. How coral reefs will respond to climate change will be a function of genetic variation and how it is partitioned within and among species. A critical initial step is to accurately delineate species and quantify their physiological potential to cope with heat stress. Cryptic species are morphologically similar but genetically distinct and may respond physiologically different to climate change. A dominant Caribbean reef builder severely affected by climate change is the mountainous star coral, <em>Orbicella faveolata</em>. Recently, Dziedzic <em>et al</em>. (2019) reported quantitative genetic variation in the physiological response to thermal stress in a single population of this species, suggesting that variation within populations will allow these corals to adapt to rising ocean temperatures. We reanalyzed their data and found multiple cryptic lineages rather than a single panmictic population, with one of the lineages being not heat-tolerant. While different cryptic lineages co-occur in certain locations, there is at least one lineage that occurs only in a single location. Our finding of hidden lineages within a threatened species highlights the varying extinction risks faced by these independently evolving groups, especially when the prospects of survival under warmer oceans seem favorable for some of them only.</p>
Hidden in the DNA: insights on how multiple historical processes and natural history traits shaped patterns of cryptic diversity in an Amazon leaf-litter lizard Loxopholis osvaldoi (Squamata: Gymnophthalmidae).
Aim: To investigate cryptic diversity and diversification timing in the putatively low-dispersal Amazonian leaf-litter lizard Loxopholis osvaldoi, and to ask how geography (rivers, isolation by distance, IBD), ecological drivers (isolation by environment, IBE) and historical factors (climatic refugia) explain intraspecific genetic variation. Location: Central Amazonia, Brazil. Taxon: Squamata; Gymnophthalmidae; Loxopholis osvaldoi. Methods: We sequenced two mitochondrial and two nuclear markers in 157 individuals. Phylogeographic structure and the occurrence of independent evolving lineages where explored through phylogenetic and coalescent analyses. A species tree and divergence dates of lineages were inferred with BEAST, employing multiple DNA substitution rates. The potential genetic impacts of geographic distance among localities, the environment, and the position of localities in relation to main rivers were tested by Redundancy Analysis (RDA). Results: We detected 11 independently evolving and largely divergent intraspecific lineages. Lineage distribution patterns are complex and do not match any conspicuous barrier to gene flow, except for the Amazon River. Most lineages appear to have originated in the lower Miocene and Pliocene, in disagreement with the Pleistocene refuge hypothesis. IBD, IBE, and rivers appear to have acted in concert establishing and maintaining genetic structure. However, when controlling for other explanatory variables, IBD explains significantly more variation than rivers, IBE, or historical factors. Main conclusions: Our results strongly suggest that L. osvaldoi is a species complex. Future taxonomic work should use an integrative approach to explore whether morphological variation is present and congruent with the genetic data. While the use of a sensitive dating analysis allowed us to better describe the diversification history of L. osvaldoi, the lack of a spatial model of Neogene river dynamics prevents the test of specific, more informative river barrier hypotheses. The data suggest that non-linear correlation analyses (e.g. RDA) should be preferred to detect factors that affect phylogeographic patterns in the Amazon, instead of linear multiple regressions (e.g. Mantel tests). Given the high level of cryptic diversity detected within this and other Amazonian species, we caution against hypothesis tests based solely on the distribution of nominal taxa, which can provide a rather incomplete view of the processes behind Amazonian diversity.
Sex-specific sterility caused by extreme temperatures is likely to create cryptic changes to the operational sex ratio in Drosophila virilis
<p>Climate change is increasing the frequency and severity of short-term heat shocks that threaten the persistence of natural populations. The effect of thermal stress on natural selection is a common topic of debate, but high temperatures can also influence sexual selection. Typically, males and females of a species can survive at similar extreme temperatures, but males have been shown to lose fertility at lower temperatures than females. Here, we examine how a brief exposure of pupae to high temperatures in the fruit fly Drosophila virilis affects adult fertility in both males and females. We find strong sexual dimorphism in temperature-induced sterility. This has the potential to quickly and unpredictably create populations composed of mostly sterile males and fertile females, resulting in changes to the operational sex ratio (OSR). These disruptions are likely to be cryptic and difficult to measure in the wild, especially considering that males can eventually recover fertility and that sterile males of some species can still copulate. Changes to the OSR in this way are likely to influence sexual selection by favouring females that can discriminate between fertile and sterilised males, and possibly leading to female-female conflict over a limited pool of fertile males. Further research on how cryptic disruptions to the OSR affect sexual selection dynamics is critical for understanding the impact of environmental change on biodiversity.</p>
Figure 2 in Integrative taxonomy resolves three new cryptic species of small southern African horseshoe bats (Rhinolophus)
Figure 2. Bayesian tree of partial Cytb sequences, with nodal support values based on Bayesian probabilities and bootstrap values for Maximum Likelihood and Maximum Parsimony. Samples included in all analyses (molecular, morphometric and bacular) are underlined.
Figure 14 in Integrative taxonomy resolves three new cryptic species of small southern African horseshoe bats (Rhinolophus)
Figure 14. Colony of R. lobatus showing present of orange apical tuft in flying males (Photographs by P. Naskrecki.)
Figure 5. Biplot showing the first and second principal components from a in Integrative taxonomy resolves three new cryptic species of small southern African horseshoe bats (Rhinolophus)
Figure 5. Biplot showing the first and second principal components from a PCA of 2D landmark data for small southern Africa Rhinolophus spp., including data from type specimens of R. swinnyi and R. s. rhodesiae. Deformation grids illustrate cranial shape changes associated with each PC.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.