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1,138 results for “cryptic diversity”
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.
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.
Figure 8. A–C in High cryptic diversity in the kleptoparasitic genus Hyalorisia Dall, 1889 (Littorinimorpha: Capulidae) with the description of nine new species from the Indo-West Pacific
Figure 8. A–C. Holotype of Capulus (Hyalorisia) galea Dall, 1889, USNM 508724, off Barbados. D–F. Holotype of Capulus (Hyalorisia) tosaensis Otuka, 1939, Seto Marine Biological Laboratory, collected from Bay of Tosa, Japan. G–I. Syntype of Capulus fragilis E. A. Smith, 1904, NHMUK 1904.6.15.136, Laccadive Sea. J. Original figure of Capulus fallax S. V. Wood, 1842 (Wood, 1842: pl. 17, fig. 4a, b), Lower Pliocene of England. K–N. Holotype of Capulus (Hyalorisia) nettlesi J. E. Robinson, 1983, PRI 30058, Upper Eocene of Mississippi. Scale bars: A–E, G–I, K–N = 10 mm; F = 5 mm. Photo credits: A–C, USNM; D–F, Kyoto University (taken by Ryutaro Goto); G–I, NHMUK (taken by Harry Taylor); K–N, Paleontological Research Institution, Ithaca, NY.
Figure 10. A–K in High cryptic diversity in the kleptoparasitic genus Hyalorisia Dall, 1889 (Littorinimorpha: Capulidae) with the description of nine new species from the Indo-West Pacific
Figure 10. A–K. Distribution of Hyalorisia species (based on our data) and of the Propeamussium host species from GBIF records (L). A. Hyalorisia galea. B. Hyalorisia kely n. sp. C. Hyalorisia lehibe n. sp. D. Hyalorisia madagascarensis n. sp. E. Hyalorisia tosaensis. F. Hyalorisia profunda n. sp. G. Hyalorisia nanhaiensis n. sp. H. Hyalorisia solomonensis n. sp. I. Hyalorisia melanesica n. sp. J. Hyalorisia neocaledonica n. sp. K. Hyalorisia nupta n. sp. L. Distribution of Propeamussium host species based on GBIF records. Ranges are given in different colours as follows: blue, P. dalli; red, P. caducum; yellow, P. watsoni; orange, P. sibogai; green, P. investigatoris; violet, P. jeffreysii. In maps A–K, Hyalorisia records are shown in the same colour as the host species to which they were attached at the time of collection (as in L), or are shown in grey, indicating that samples were not collected directly from a host.
Figure 6 in High cryptic diversity in the kleptoparasitic genus Hyalorisia Dall, 1889 (Littorinimorpha: Capulidae) with the description of nine new species from the Indo-West Pacific
Figure 6. Shells of Hyalorisia (A–C) and detail of the lamella (D, E). A. Hyalorisia profunda, holotype, MNHN-IM-2013-59695, South China Sea (L = 7 mm). B. Hyalorisia madagascarensis n. sp., holotype, MNHN-IM-2007-39090, off Mahajanga, Madagascar (L = 6.5 mm). C. Hyalorisia solomonensis n. sp., holotype, MNHN-IM-2007-34203, SE of Santa Isabel, Solomon Islands (L = 8 mm). D. Wide lamella of Hyalorisia neocaledonica n. sp., MNHN-IM-2013-65645, Lord Howe Rise, New Caledonia. E. Narrow lamella of Hyalorisia tosaensis, MNHN-IM-2013-58352, New Ireland, Papua New Guinea. Scale bars = 2 mm.
Figure 4 in High cryptic diversity in the kleptoparasitic genus Hyalorisia Dall, 1889 (Littorinimorpha: Capulidae) with the description of nine new species from the Indo-West Pacific
Figure 4. Shells of Hyalorisia. A. Hyalorisia galea, MNHN-IM-2013-60195, N of Grande-Terre, Guadeloupe (L = 13 mm). B. Hyalorisia neocaledonica n. sp., holotype, MNHN-IM-2013-65645, Lord Howe Rise, New Caledonia (L = 9.5 mm). C. Hyalorisia tosaensis, MNHN-IM-2013-58352, New Ireland, Papua New Guinea (L = 15 mm). D. Hyalorisia nupta n. sp., holotype, MNHN-IM-2007-34010, Bellona Reefs, New Caledonia (L = 18.5 mm). Scale bars = 2 mm.
Figure 5 in High cryptic diversity in the kleptoparasitic genus Hyalorisia Dall, 1889 (Littorinimorpha: Capulidae) with the description of nine new species from the Indo-West Pacific
Figure 5. Shells of Hyalorisia. A. Hyalorisia lehibe n. sp., holotype, MNHN-IM-2007-39212, off Mahajanga, Madagascar (L = 15 mm). B. Hyalorisia nanhaiensis n. sp., holotype, MNHN-IM-2013-59534, S of Dongsha (=Pratas) Islands, South China Sea (L = 8.5 mm). C. Hyalorisia kely n. sp., holotype, MNHN-IM-2007-39091, off Mahajanga, Madagascar (L = 6.5). D. Hyalorisia melanesica n. sp., holotype, MNHN-IM-2007-33873, Bellona Reefs, New Caledonia (L = 6.6 mm). Scale bars = 2 mm.
Figure 9 in High cryptic diversity in the kleptoparasitic genus Hyalorisia Dall, 1889 (Littorinimorpha: Capulidae) with the description of nine new species from the Indo-West Pacific
Figure 9. Bivalve hosts (Propeamussium spp.) with foot mark (black arrows) and notch (white arrows) of Hyalorisia. A. Propeamussium sibogai, MNHN-IM-2007- 33954 (L = 46.7 mm), host of H. nupta n. sp. (MNHN-IM-2007-34010). B. Propeamussium caducum, MNHN-IM-2007-39095 (L = 17.8 mm), host of H. kely n. sp. (MNHN-IM-2007-39091). C, D. Propeamussium dalli, MNHN-IM-2013-60196 (L = 83 mm) with H. galea (MNHN-IM-2013-60195) still attached. Photo credits: MNHN; taken by Yves Terryn (A, B) and Laurent Charles (C). Scale bars = 5 mm.
Figure 7 in High cryptic diversity in the kleptoparasitic genus Hyalorisia Dall, 1889 (Littorinimorpha: Capulidae) with the description of nine new species from the Indo-West Pacific
Figure 7. Radulae of Hyalorisia (A–I) and detail of the rachidian tooth (J–R). A, J. Hyalorisia galea MNHN-IM-2013-60195. B, K. Hyalorisia neocaledonica n. sp., MNHN-IM-2013-65647. C, L. Hyalorisia tosaensis, MNHN-IM-2013-58352. D, M. Hyalorisia nupta n. sp., MNHN-IM-2013-68952. E, N. Hyalorisia nanhaiensis n. sp., MNHN-IM-2013-59697. F, O. Hyalorisia kely n. sp., MNHN-IM-2007-38809. G, P. Hyalorisia melanesica n. sp., MNHN-IM-2007-34205. H, Q. Hyalorisia madagascarensis n. sp., MNHN-IM-2007-39090. I, R. Hyalorisia solomonensis n. sp., MNHN-IM-2007-34215. Scale bars = 100 µm.
Figure 2 in High cryptic diversity in the kleptoparasitic genus Hyalorisia Dall, 1889 (Littorinimorpha: Capulidae) with the description of nine new species from the Indo-West Pacific
Figure 2. Phylogenetic relationships of the genus Hyalorisia (Bayesian tree based on the combined dataset). Boxes indicate the three lineages, A, B and C, of Hyalorisia. Numbers at nodes are PP and UFb branch support values, respectively; only values higher than 80% are reported, and black dots indicate maximally supported branches. Scale bar indicates substitutions per site.
Figure 1 in High cryptic diversity in the kleptoparasitic genus Hyalorisia Dall, 1889 (Littorinimorpha: Capulidae) with the description of nine new species from the Indo-West Pacific
Figure 1. Phylogenetic relationships of the genus Hyalorisia (Bayesian tree based on the COI dataset). Numbers at nodes indicate branch support values (PP and UFb values, respectively); only values ≥95% are shown. Boxes indicate the final species hypotheses (MOTUs) for the genus. The histogram displays the distribution of the pairwise genetic distances (K2P) for the MOTUs, as based on the COI alignment; the black bars on the left are intraspecific distances and the yellow bars on the right are interspecific distances. The last two letters in the sample codes indicate the relevant general area of origin: ANT, Antarctica; JP, Japan; AK, Alaska; WA, Washington State; CA, California; PH, Philippines; NC, New Caledonia; SE, Sweden; IT, Italy; FR, Corsica; CNSea, South China Sea; MZChannel, Mozambique Channel; MG, Madagascar; PG, Papua New Guinea; SB, Solomon Islands; GP, Guadeloupe. Scale bar indicates substitutions per site.
Figure 3 in High cryptic diversity in the kleptoparasitic genus Hyalorisia Dall, 1889 (Littorinimorpha: Capulidae) with the description of nine new species from the Indo-West Pacific
Figure 3. Protoconchs of Hyalorisia. A. Hyalorisia galea, MNHN-IM-2013-61536. B. Hyalorisia neocaledonica n. sp., MNHN-IM-2013-65907. C. Hyalorisia tosaensis, MNHN-IM-2007-34794. D. Hyalorisia nupta n. sp., MNHN-IM-2007-34005. E. Hyalorisia lehibe n. sp., MNHN-IM-2007-39212. F. Hyalorisia nanhaiensis n. sp., MNHN-IM-2013-34796. G. Hyalorisia kely n. sp., MNHN-IM-2007-38809. H. Hyalorisia melanesica n. sp., MNHN-IM-2013-58359. I. Hyalorisia profunda n. sp., MNHN-IM-2007-33828. J. Hyalorisia madagascarensis n. sp., MNHN-IM-39292. K. Hyalorisia solomonensis n. sp., MNHN-IM-2007-34215. Scale bars = 100 µm.
Data from: Cryptic diversity hides host and habitat specialization In a gorgonian-algal symbiosis
Shallow water anthozoans, the major builders of modern coral reefs, enhance their metabolic and calcification rates with algal symbionts. Controversy exists over whether these anthozoan-algae associations are flexible over the lifetimes of individual hosts, promoting acclimative plasticity, or are closely linked, such that hosts and symbionts coevolve across generations. Given the diversity of algal symbionts and the morphological plasticity of many host species, cryptic variation within either partner could potentially confound studies of anthozoan-algal associations. Here, we used ribosomal, organelle, and nuclear sequences, along with microsatellite variation, to study the relationship between lineages of a common Caribbean gorgonian and its algal symbionts. The gorgonian Eunicea flexuosa is a broadcast spawner, composed of two recently diverged, genetically distinct lineages largely segregated by depth. We sampled colonies of the two lineages across depth gradients at three Caribbean locations. We find that each host lineage is associated with a unique Symbiodinium B1/184 phylotype. This relationship between host and symbiont is maintained when host colonies are reciprocally transplanted, although cases of within phylotype switching were also observed. Even when the phylotypes of both partners are present at intermediate depths, the specificity between host and symbiont lineages remained absolute. Unrecognized cryptic diversity may mask host-symbiont specificity and change the inference of evolutionary processes in mutualistic associations. Symbiotic specificity thus likely contributes to the ecological divergence of the two partners, generating species diversity within coral reefs.
Data from: In the shadows: phylogenomics and coalescent species delimitation unveil cryptic diversity in a Cerrado endemic lizard (Squamata: Tropidurus)
The recognition of cryptic diversity within geographically widespread species is gradually becoming a trend in the highly speciose Neotropical biomes. The statistical methods to recognise such cryptic lineages are rapidly advancing, but have rarely been applied to genomic-scale datasets. Herein, we used phylogenomic data to investigate phylogenetic history and cryptic diversity within Tropidurus itambere, a lizard endemic to the Cerrado biodiversity hotspot. We applied a series of phylogenetic methods to reconstruct evolutionary relationships and a coalescent Bayesian species delimitation approach (BPP) to clarify species limits. The BPP results suggest that the widespread nominal taxon comprises a complex of 5 highly supported and geographically structured cryptic species. We highlight and discuss the different topological patterns recovered by concatenated and coalescent species tree methods for these closely related lineages. Finally, we suggest that the existence of cryptic lineages in the Cerrado is much more common than traditionally thought, highlighting the value of using NGS data and coalescent techniques to investigate patterns of species diversity.
Data from: Multilocus phylogeny and Bayesian estimates of species boundaries reveal hidden evolutionary relationships and cryptic diversity in Southeast Asian monitor lizards
Recent conceptual, technological, and methodological advances in phylogenetics have enabled increasingly robust statistical species delimitation in studies of biodiversity. As the variety of evidence purporting species diversity has increased, so too have the kinds of tools and inferential power of methods for delimiting species. Here we showcase an organismal system for a data-rich, comparative molecular approach to evaluating strategies of species delimitation among monitor lizards of the genus Varanus. The water monitors (Varanus salvator Complex), a widespread group distributed throughout Southeast Asia and southern India, have been the subject of numerous taxonomic treatments, which have drawn recent attention due to the possibility of undocumented species diversity. To date, studies of this group have relied on purportedly diagnostic morphological characters, with no attention given to the genetic underpinnings of species diversity. Using a 5-gene dataset, we estimated phylogeny and used multilocus genetic networks, analysis of population structure, and a Bayesian coalescent approach to infer species boundaries. Our results contradict previous systematic hypotheses, reveal surprising relationships between island and mainland lineages, and uncover novel, cryptic evolutionary lineages (i.e. new putative species). Our study contributes to a growing body of literature suggesting that, used in concert with other sources of data (e.g., morphology, ecology, biogeography), multilocus genetic data can be highly informative to systematists and biodiversity specialists when attempting to estimate species diversity and identify conservation priorities. We recommend holding in abeyance taxonomic decisions until multiple, converging lines of evidence are available to best inform taxonomists, evolutionary biologists, and conservationists.
Data from: Cryptic diversity in a fig wasp community – morphologically differentiated species are sympatric but cryptic species are allopatric
A key debate in ecology centres on the relative importance of niche and neutral processes in determining patterns of community assembly with particular focus on whether ecologically similar species with similar functional traits are able to coexist. Meanwhile, molecular studies are increasingly revealing morphologically indistinguishable cryptic species with presumably similar ecological roles. Determining the geographic distribution of such cryptic species provides opportunities to contrast predictions of niche versus neutral models. Discovery of sympatric cryptic species increases alpha diversity and supports neutral models, while documentation of allopatric/parapatric cryptic species increases beta diversity and supports niche models. We tested these predictions using morphological and molecular data, coupled with environmental niche modelling analyses, of a fig wasp community along its 2700 km latitudinal range. Molecular methods increased previous species diversity estimates from eight to eleven species, revealing morphologically cryptic species in each of the four wasp genera studied. Congeneric species pairs that were differentiated by a key morphological functional trait (ovipositor length) coexisted sympatrically over large areas. In contrast, morphologically similar species, with similar ovipositor lengths, typically showed parapatric ranges with very little overlap. Despite parapatric ranges, environmental niche models of cryptic congeneric pairs indicate large regions of potential sympatry, suggesting that competitive processes are important in determining the distributions of ecologically similar species. Niche processes appear to structure this insect community and cryptic diversity may typically contribute mostly to beta rather than alpha diversity.
Data from: Global analysis reveals that cryptic diversity is linked with habitat but not mode of life
The ubiquity of genetically distinct, cryptic species is limiting any attempt to estimate local or global biodiversity as well as impeding efforts to conserve species or control pests and diseases. Environmental factors or biological traits promoting rapid diversification into morphologically similar species remain unclear. Here, using a meta-analysis of 1230 studies using DNA sequences to search for cryptic diversity in metazoan taxa, we test two hypotheses regarding the frequency of cryptic taxa based on mode of life and habitat. First, after correcting for study effort and accounting for higher taxonomic affinities and biogeographical region of origins, our results do not support the hypothesis that cryptic taxa are more frequent among parasitic than free-living taxa. Second, in contrast the results support the hypothesis that cryptic taxa are more common in certain habitats than others: for a given study effort, more cryptic taxa are found in freshwater than in terrestrial or marine taxa. These findings suggest that the greater heterogeneity and fragmentation of freshwater habitats may promote higher rates of genetic differentiation among its inhabitants, a general pattern with serious implications for freshwater conservation biology.
Data from: Strong spatial structure, Pliocene diversification and cryptic diversity in the Neotropical dry forest spider Sicarius cariri
The Brazilian Caatinga is part of the seasonally dry tropical forests, a vegetation type disjunctly distributed throughout the Neotropics. It has been suggested that during Pleistocene glacial periods, these dry forests had a continuous distribution, so that these climatic shifts may have acted as important driving forces of the Caatinga biota diversification. To address how these events affected the distribution of a dry forest species, we chose Sicarius cariri, a spider endemic to the Caatinga, as a model. We studied the phylogeography of one mitochondrial and one nuclear gene and reconstructed the paleodistribution of the species using modelling algorithms. We found two allopatric and deeply divergent clades within S. cariri, suggesting that this species as currently recognized might consist of more than one independently evolving lineage. Sicarius cariri populations are highly structured, with low haplotype sharing among localities, high fixation index and isolation by distance. Models of paleodistribution, Bayesian reconstructions and coalescent simulations suggest that this species experienced a reduction in its population size during glacial periods, rather than the expansion expected by previous hypotheses on the paleodistribution of dry forest taxa. In addition to that, major splits of intraspecific lineages of S. cariri took place in the Pliocene. Taken together, these results indicate S. cariri has a complex diversification history dating back to the Tertiary, suggesting the history of dry forest taxa may be significantly older than previously thought.
Cryptic diversity across the Trans-Mexican Volcanic Belt of Mexico in the montane bunchgrass lizard Sceloporus subniger (Squamata: Phrynosomatidae)
<p><em>Sceloporus subniger</em> Poglaygen & Smith is a montane bunchgrass lizard distributed across pine-oak forests of central Mexico. Prompted by the discovery of a new population of this lizard in far western Mexico, and by recent studies suggesting <em>S. subniger</em> may be a composite of several distinct species, we examined in more detail the genetic structure of <em>S. subniger</em>. We generated a mitochondrial DNA (mtDNA) dataset from 81 specimens and an ultraconserved elements (UCE) dataset representing thousands of genomic regions from 12 specimens to specifically evaluate the genetic distinctiveness of populations from western Michoacán and adjacent Jalisco along with the newly discovered population in the Sierra de Mascota in western Jalisco. We also recorded morphological data from 47 museum specimens to compare to our genetic data. Results from our analyses of the genetic data, augmented by specimen measurements and scale counts, support the notion that <em>S. subniger</em> is indeed a composite of distinct species. Montane bunchgrass lizards from western Michoacán and adjacent Jalisco, and from the Sierra de Mascota in western Jalisco, each represent distinct new species, which we describe and name here.</p>
Data from: Are pheromones key to unlocking cryptic lizard diversity?
Animals use mating traits to compete for, attract, and choose mates. Because mating traits influence mate choice, the divergence of mating traits between populations can result in reproductive isolation. This can occur without associated morphological divergence, producing reproductively isolated 'cryptic species' that are visually indistinguishable. Thus, identifying the mating traits in morphologically conservative groups is key to resolving diversity and speciation processes. Lizards contain many such groups, with phylogeographic studies often revealing highly divergent but morphologically cryptic lineages within species. Considering that cryptic lizard species can be sympatric but morphologically indistinguishable, we hypothesize that candidate species will exhibit divergent pheromones and that pheromones will have typically diverged more than morphology. To test this, we used gas chromatography to characterize pheromones (epidermal pore secretions) from 10 genetically divergent lineages of the Bynoe's gecko (Heteronotia binoei) species complex in northern Australia. Multivariate analyses of pheromone blends and morphology indicate that pheromones are lineage-specific and have diverged relatively more than morphology. Such specificity suggests that pheromones influence behavioral isolation in this morphologically conservative lizard radiation. These results suggest that pheromone data may unlock the tremendous 'cryptic' diversity currently being uncovered in many lizard groups.
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