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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.

opencc-zeroDec 2016View details →

Data from: Range instability leads to cytonuclear discordance in a morphologically cryptic ground squirrel species complex

The processes responsible for cytonuclear discordance frequently remain unclear. Here, we employed an exon capture dataset and demographic methods to test hypotheses generated by species distribution models to examine how contrasting histories of range stability vs. fluctuation have caused cytonuclear concordance and discordance in ground squirrel lineages from the Otospermophilus beecheyi species complex. Previous studies in O. beecheyi revealed three morphologically cryptic and highly divergent mitochondrial DNA lineages (named the Northern, Central, and Southern lineages based on geography) with only the Northern lineage exhibiting concordant divergence for nuclear genes. Here, we showed that these mtDNA lineages likely formed in allopatry during the Pleistocene, but responded differentially to climatic changes that occurred since the last interglacial (~120,000 years ago). We find that the Northern lineage maintained a stable range throughout this period, correlating with genetic distinctiveness among all genetic markers and low migration rates with the other lineages. In contrast, our results suggested that the Southern lineage expanded from Baja California Sur during the Late Pleistocene to overlap and potentially swamp a contracting Central lineage. High rates of intraspecific gene flow between Southern lineage individuals among expansion origin and expansion edge populations largely eroded Central ancestry from autosomal markers. However, male-biased dispersal in this system preserved signals of this past hybridization and introgression event in matrilineal-biased X-chromosome and mtDNA markers. Our results highlight the importance of range stability in maintaining the persistence of phylogeographic lineages, whereas unstable range dynamics can increase the tendency for lineages to merge upon secondary contact.

opencc-zeroDec 2012View details →

Data from: Reproductive isolation and patterns of genetic differentiation in a cryptic butterfly species complex

Molecular studies of natural populations are often designed to detect and categorize hidden layers of cryptic diversity, and an emerging pattern suggests that cryptic species are more common and more widely distributed than previously thought. However, these studies are often decoupled from ecological and behavioural studies of species divergence. Thus, the mechanisms by which the cryptic diversity is distributed and maintained across large spatial scales are often unknown. In 1988, it was discovered that the common Eurasian Wood White butterfly consisted of two species (Leptidea sinapis and Leptidea reali), and the pair became an emerging model for the study of speciation and chromosomal evolution. In 2011, the existence of a third cryptic species (Leptidea juvernica) was proposed. This unexpected discovery raises questions about the mechanisms preventing gene flow and about the potential existence of additional species hidden in the complex. Here, we compare patterns of genetic divergence across western Eurasia in an extensive data set of mitochondrial and nuclear DNA sequences with behavioural data on inter- and intraspecific reproductive isolation in courtship experiments. We show that three species exist in accordance with both the phylogenetic and biological species concepts and that additional hidden diversity is unlikely to occur in Europe. The Leptidea species are now the best studied cryptic complex of butterflies in Europe and a promising model system for understanding the formation of cryptic species and the roles of local processes, colonization patterns and heterospecific interactions for ecological and evolutionary divergence.

opencc-zeroDec 2014View details →

Data from: Are generalist Aphidiinae (Hym. Braconidae) mostly cryptic species complexes?

Aphidiinae are mostly composed of specialist parasitoids and the few species described as generalist are suspected to be composed of cryptic specialists, almost indistinguishable based on morphological characteristics. The use of molecular markers has proven to be a useful tool for revealing cryptic species complexes and here we use seven mitochondrial and nuclear gene fragments to study possible genetic differentiation among seven Aphidiinae generalists. Maximum likelihood (ML) trees and Bayesian Poisson tree processes (bPTP) models were conducted on each gene separately and on the seven genes together. The standard cytochrome c oxidase I barcode region appeared to be the most polymorphic and probably the best marker to reveal putative cryptic species. However, we showed with ML trees and bPTP models that a complementary use of mitochondrial and nuclear genes was the most relevant approach to reliably identify cryptic genetic clades in the Aphidiinae. Overall, most of the analysed generalist morphospecies were shown to be composed of subgroups related to the aphid host, some of them revealed as cryptic species by the species delimitation analysis. Further studies are needed to reveal the generality of this result in Aphidiinae.

opencc-zeroDec 2015View details →

Data from: Integrative taxonomy recognizes evolutionary units despite widespread mitonuclear discordance: evidence from a rotifer cryptic species complex

Mitonuclear discordance across taxa is increasingly recognized as posing a major challenge to species delimitation based on DNA sequence data. Integrative taxonomy has been proposed as a promising framework to help address this problem. However, we still lack compelling empirical evidence scrutinizing the efficacy of integrative taxonomy in relation to, for instance, complex introgression scenarios involving many species. Here, we report remarkably widespread mitonuclear discordance between about 15 mitochondrial and four nuclear Brachionus calyciflorus groups identified using different species delimitation approaches. Using coalescent-, Bayesian admixture-, and allele sharing-based methods with DNA sequence or microsatellite data, we provide strong evidence in support of hybridization as a driver of the observed discordance. We then describe our combined molecular, morphological, and ecological approaches to resolving phylogenetic conflict and inferring species boundaries. Species delimitations based on the ITS1 and 28S nuclear DNA markers proved a more reliable predictor of morphological variation than delimitations using the mitochondrial COI gene. A short-term competition experiment further revealed systematic differences in the competitive ability between two of the nuclear-delimited species under six different growth conditions, independent of COI delimitations; hybrids were also observed. In light of these findings, we discuss the failure of the COI marker to estimate morphological stasis and morphological plasticity in the B. calyciflorus complex. By using B. calyciflorus as a representative case, we demonstrate the potential of integrative taxonomy to guide species delimitation in the presence of mitonuclear phylogenetic conflicts.

opencc-zeroDec 2016View details →

Data from: Divergent clades or cryptic species? Mito-nuclear discordance in a Daphnia species complex

Background: Genetically divergent cryptic species are frequently detected by molecular methods. These discoveries are often a byproduct of molecular barcoding studies in which fragments of a selected marker are used for species identification. Highly divergent mitochondrial lineages and putative cryptic species are even detected in intensively studied animal taxa, such as the crustacean genus Daphnia. Recently, eleven such lineages, exhibiting genetic distances comparable to levels observed among well-defined species, were recorded in the D. longispina species complex, a group that contains several key taxa of freshwater ecosystems. We tested if three of those lineages represent indeed distinct species, by analyzing patterns of variation of ten nuclear microsatellite markers in six populations. Results: We observed a discordant pattern between mitochondrial and nuclear DNA, as all individuals carrying one of the divergent mitochondrial lineages grouped at the nuclear level with widespread, well-recognized species coexisting at the same localities (Daphnia galeata, D. longispina, and D. cucullata). Conclusions: A likely explanation for this pattern is the introgression of the mitochondrial genome of undescribed taxa into the common species, either in the distant past or after long-distance dispersal. The occurrence of highly divergent but rare mtDNA lineages in the gene pool of widespread species would suggest that hybridization and introgression in the D. longispina species complex is frequent even across large phylogenetic distances, and that discoveries of such distinct clades must be interpreted with caution. However, maintenance of ancient polymorphisms through selection is another plausible alternative that may cause the observed discordance and cannot be entirely excluded.

opencc-zeroDec 2013View details →

Data from: Global biodiversity assessment and hyper-cryptic species complexes: more than one species of elephant in the room?

Several recent estimates of global biodiversity have concluded that the total number of species on Earth lies near the lower end of the wide range touted in previous decades. However, none of these recent estimates formally explore the real 'elephant in the room', namely, what proportion of species are taxonomically invisible to conventional assessments, and thus, as undiagnosed cryptic species, remain uncountable until revealed by multi-gene molecular assessments. Here we explore the significance and extent of so-called 'hyper-cryptic' species complexes, using the Australian freshwater fish Galaxias olidus as a proxy for any organism whose taxonomy ought to be largely finalized when compared to those in little-studied or morphologically undifferentiated groups. Our comprehensive allozyme (838 fish for 54 putative loci), mtDNA (557 fish for 605bp of cytb), and morphological (1963–3389 vouchers for 17–58 characters) assessment of this species across its broad geographic range revealed a 1500% increase in species-level biodiversity, and suggested that additional taxa may remain undiscovered. Importantly, while all 15 candidate species were morphologically diagnosable a posteriori from one another, single-gene DNA barcoding proved largely unsuccessful as an a priori method for species identification. These results lead us to draw two strong inferences of relevance to estimates of global biodiversity. First, hyper-cryptic complexes are likely to be common in many organismal groups. Second, no assessment of species numbers can be considered 'best practice' in the molecular age unless it explicitly includes estimates of the extent of cryptic and hyper-cryptic biodiversity.

opencc-zeroDec 2012View details →

Data from: Integrative taxonomy resolves the cryptic and pseudo-cryptic Radula buccinifera complex (Porellales: Jungermanniopsida), including two reinstated and five new species

Molecular data from three chloroplast markers resolve individuals attributable to Radula buccinifera in six lineages belonging to two subgenera, indicating the species is polyphyletic as currently circumscribed. All lineages are morphologically diagnosable, but one pair exhibits such morphological overlap that they can be considered cryptic. Molecular and morphological data justify the re-instatement of a broadly circumscribed ecologically variable R. strangulata, of R. mittenii, and the description of five new species. Two species Radula mittenii Steph. and R. notabilis sp. nov. are endemic to the Wet Tropics Bioregion of north-east Queensland, suggesting high diversity and high endemism might characterise the bryoflora of this relatively isolated wet-tropical region. Radula demissa sp. nov. is endemic to southern temperate Australasia, and like R. strangulata occurs on both sides of the Tasman Sea. Radula imposita sp. nov. is a twig and leaf epiphyte found in association with waterways in New South Wales and Queensland. Another species, R. pugioniformis sp. nov., has been confused with Radula buccinifera but was not included in the molecular phylogeny. Morphological data suggest it may belong to subg. Odontoradula. Radula buccinifera is endemic to Australia including Western Australia and Tasmania, and to date is known from south of the Clarence River on the north coast of New South Wales. Nested within R. buccinifera is a morphologically distinct plant from Norfolk Island described as R. anisotoma sp. nov. Radula australiana is resolved as monophyletic, sister to a species occurring in east coast Australian rainforests, and nesting among the R. buccinifera lineages with strong support. The molecular phylogeny suggests several long-distance dispersal events may have occurred. These include two east-west dispersal events from New Zealand to Tasmania and south-east Australia in R. strangulata, one east-west dispersal event from Tasmania to Western Australia in R. buccinifera, and at least one west-east dispersal from Australia to New Zealand in R. australiana. Another west-east dispersal event from Australia to Norfolk Island may have led to the budding speciation of R. anisotoma. In contrast, Radula demissa is phylogeographically subdivided into strongly supported clades either side of the Tasman Sea, suggesting long distance dispersal is infrequent in this species.

opencc-zeroOct 2019View details →

Lack of habitat segregation and no interspecific territoriality in three syntopic cryptic species of the golden-spectacled warblers Phylloscopus (Seicercus) burkii complex

<p>It is widely accepted that exploitative competition prevents the coexistence of any two or more closely-related species unless differences exists in their ecological niches and resource use. In sibling bird species, exploitative competition is reduced mainly by spatial segregation of competing species. Spatial segregation can be achieved in two basic ways: by using different habitats or microhabitats that each species is predominately exploiting, or by interspecific territoriality. To our knowledge, either habitat segregation or interspecific territoriality or both have been found in all dyads and groups of sympartic sibling bird species studied so far. In this study, we investigated the coexistence of three cryptic sibling species of the golden-spectacled warblers Phylloscopus burkii complex in Hunan province, China: Ph. tephrocephalus, Ph. omeiensis and Ph. valentini. We analyzed their habitat preferences, and spatial interrelations between the species. In order to analyze either presence or absence of interspecific territoriality, we additionally performed con- and heterospecific playback experiments. Contrary to expectations, we found no evidences for either habitat segregation or interspecific territoriality in these three species.</p>

opencc-zeroDec 2016View details →

Data from: Cryptic speciation and gene flow in a migratory songbird species complex: insights from the red-eyed vireo (Vireo olivaceus)

Migratory species that alternate between sympatry and allopatry over the course of an annual cycle are promising subjects for studies seeking to understand the process of speciation in the absence of strict geographic isolation. Here we sought to identify cryptic species and assess rates of gene flow in a clade of neotropical migrant songbirds in which geography and taxonomy are currently out of sync: the Red-Eyed Vireo (V. olivaceus) Species Complex. Phylogenetic, clustering, and statistical species delimitation analyses found that V. olivaceus includes two non-sister lineages migrating in opposite directions across the equator. Analyses of gene flow identified low levels of introgression between two species pairs, but none between northern and southern olivaceus. We also identified substantial well-supported conflicts between nuclear and mitochondrial topologies. Although the geographic distribution of mito-nuclear discordance is suggestive of hybridization and mitochondrial capture, we found no evidence of introgression in the nuclear genome of populations with discordant mitochondrial gene trees. Our study finds that species boundaries match breeding range and migratory phenology rather than the existing taxonomy in this group, and demonstrates the utility of genomic data in inferring species boundaries in recently diverged clades.

FIGURE 1 in A partial revision of the Ameerega hahneli complex (Anura: Dendrobatidae) and a new cryptic species from the East-Andean versant of Central Peru

FIGURE 1. Ameerega altamazonica, dorsal and ventral views of same specimens. Top row, left to right: MUSM 26934, 26935 (Chazuta); MUSM 26936–26939 (near Tarapoto); ECU-F 107 (Tocache, non-paratype); second row, left to right: ECU-F 108-111 (Tocache, non-paratypes); MUSM 26974 (Saposoa); MUSM 26977 (Huicungo); MUSM 26981, 26982 (Campanilla); 646 (Tocache); ventral photos are in the same order. Bar in bottom center represents 10 mm.

FIGURE 4 in A partial revision of the Ameerega hahneli complex (Anura: Dendrobatidae) and a new cryptic species from the East-Andean versant of Central Peru

FIGURE 4. Lateral view (right) and oral disc (left) of tadpole of Ameerega altamazonica from Chazuta, San Martín, Peru. Bar under tadpole represents 10 mm and under oral disc 1 mm.

FIGURE 5 in A partial revision of the Ameerega hahneli complex (Anura: Dendrobatidae) and a new cryptic species from the East-Andean versant of Central Peru

FIGURE 5. Niche prediction models of Ameerega altamazonica and A. hahneli generated with Maxent. Warmer colors shows more suitable habitat than colder ones. White triangles represent presence points used in generating niche models. (A) Predicted niche of A. hahneli, (B) Predicted niche of A. altamazonica with magnified inset of central Peru (C). Test AUC values for A. altamazonica and A. hahneli were 0.999 and 0.891, respectively, suggesting high accuracy of models.

FIGURE 6 in A partial revision of the Ameerega hahneli complex (Anura: Dendrobatidae) and a new cryptic species from the East-Andean versant of Central Peru

FIGURE 6. Phylogenetic tree showing the Maximum Likelihood topology of genus Ameerega using mtDNA (12s rRNA, 16s rRNA and cytochrome b).

FIGURE 3 in A partial revision of the Ameerega hahneli complex (Anura: Dendrobatidae) and a new cryptic species from the East-Andean versant of Central Peru

FIGURE 3. (A) Advertisement call of Ameerega altamazonica, recorded at type locality 9 June 2007 at 23° C. (B) Advertisement call of A. hahneli sensu stricto, recording of captive male from 56 km S Iquitos, Peru, at 24° C. (C) Advertisement call of A. hahneli sensu stricto, individual from Bolivia (recording made available by S. Lötters). (D) Aggressive call of A. altamazonica, recorded at type locality 9 June 2007 at 23° C.