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Appendix 5 in Morphometry and DNA barcoding reveal cryptic diversity in the genus Enteromius (Cypriniformes: Cyprinidae) from the Congo basin, Africa

Appendix 5. PC loadings of the PCA in Fig. 6. Most important loadings indicated in bold.

Appendix 2 in Morphometry and DNA barcoding reveal cryptic diversity in the genus Enteromius (Cypriniformes: Cyprinidae) from the Congo basin, Africa

Appendix 2. PC loadings of the PCA in Fig. 3. Most important loadings indicated in bold.

Appendix 4 in Morphometry and DNA barcoding reveal cryptic diversity in the genus Enteromius (Cypriniformes: Cyprinidae) from the Congo basin, Africa

Appendix 4. PC loadings of the PCA in Fig. 5. Most important loadings indicated in bold.

Appendix 3 in Morphometry and DNA barcoding reveal cryptic diversity in the genus Enteromius (Cypriniformes: Cyprinidae) from the Congo basin, Africa

Appendix 3. PC loadings of the PCA in Fig. 4. Most important loadings indicated in bold.

opencc-zeroJun 2020View details →

Data from: Chemical signals from eggs facilitate cryptic female choice in humans

Mate choice can continue after mating via chemical communication between the female reproductive system and sperm. While there is a growing appreciation that females can bias sperm use and paternity by exerting cryptic female choice for preferred males, we know surprisingly little about the mechanisms underlying these post-mating choices. In particular, whether chemical signals released from eggs (chemoattractants) allow females to exert cryptic female choice to favour sperm from specific males remains an open question, particularly in species (including humans) where adults exercise pre-mating mate choice. Here, we adapt a classic dichotomous mate choice assay to the microscopic scale to assess gamete-mediated mate choice in humans. We examined how sperm respond to follicular fluid, a source of human sperm chemoattractants, from either their partner or a non-partner female when experiencing a simultaneous or non-simultaneous choice between follicular fluids. We report robust evidence under these two distinct experimental conditions that follicular fluid from different females consistently and differentially attracts sperm from specific males. This chemoattractant-moderated choice of sperm offers eggs an avenue to exercise independent mate preference. Indeed, gamete-mediated mate choice did not reinforce pre-mating human mate choice decisions. Our results demonstrate that chemoattractants facilitate gamete-mediated mate choice in humans, which offers females the opportunity to exert cryptic female choice for sperm from specific males.

opencc-zeroJul 2020View details →

Data from: Environmental change, if unaccounted, prevents detection of cryptic evolution in a wild population

Detecting contemporary evolution requires demonstrating that genetic change has occurred. Mixed-effects models allow estimation of quantitative genetic parameters and are widely used to study evolution in wild populations. However, predictions of evolution based on these parameters frequently fail to match observations. Furthermore, such studies often lack an independent measure of evolutionary change against which to verify predictions. Here, we applied three commonly used quantitative genetic approaches to predict the evolution of size at maturity in a wild population of Trinidadian guppies. Crucially, we tested our predictions against evolutionary change observed in common garden experiments performed on samples from the same population. We show that standard quantitative genetic models underestimated or failed to detect the cryptic evolution of this trait as demonstrated by the common garden experiments. The models failed because: 1) size at maturity and fitness both decreased with increases in population density, 2) offspring experienced higher population densities than their parents, and 3) selection on size was strongest at high densities. When we accounted for environmental change, predictions better matched observations in the common garden experiments, although substantial uncertainty remained. Our results demonstrate that predictions of evolution are unreliable if environmental change is not appropriately captured in models.

opencc-zeroJul 2020View details →

Data from: Cryptic patterns of speciation in cryptic primates: microendemic mouse lemurs and the multispecies coalescent

Species delimitation is ever more critical for assessing biodiversity in threatened regions of the world, especially when undescribed lineages may be at risk from habitat loss. Mouse lemurs (Microcebus) are an example of a rapid radiation of morphologically cryptic species that are distributed throughout Madagascar in its rapidly vanishing forested habitats. Here, we focus on two pairs of sister lineages that occur in a region in northeastern Madagascar that shows high levels of microendemism. We revisit previous hypotheses of species diversity by filling geographic sampling gaps and by generating new genomic data for three named species, as well as an undescribed lineage previously identified to be of interest due to its highly divergent mtDNA. We analyzed RADseq data with multiple species delimitation methods based on the multispecies coalescent (MSC) model while accounting for introgression. Non-sister lineages occur sympatrically in two instances, despite an estimated divergence time of less than 1 Ma, thus suggesting rapid evolution of reproductive isolation in the mouse lemur clade. We note, however, that the divergence time estimates reported here are based on the MSC and calibrated with pedigree-based primate mutation rates. These dates are considerably more recent than previous analyses that used traditional relaxed clock methods and distant fossil calibrations. One pair of sister lineages passed all species delimitation tests while the other pair failed most, largely due to differences in Ne between the two pairs of lineages. Nevertheless, delimitation results were also supported by differences in levels of gene flow and patterns of isolation-by-distance between the two pairs. We conclude that MSC-based species delimitation methods are valuable tools for evaluating cryptic species, even though these methods can be strongly affected by variable Ne. We suggest that this result has general implications for species delimitation studies of other recently diverged lineages.

opencc-zeroAug 2020View details →

Data from: Large-scale mutation in the evolution of a gene complex for cryptic coloration

The types of mutations affecting adaptation in the wild are only beginning to be understood. In particular, whether structural changes shape adaptation by suppressing recombination or by creating new mutations is unresolved. Here we show that multiple, linked but recombining loci underlie cryptic color morphs of Timema chumash stick insects. In a related species, these loci are found in a region of suppressed recombination, forming a supergene. However, in seven species of Timema we find that a mega-base size 'supermutation' has deleted color loci in green morphs. Moreover, we find that balancing selection likely contributes more to maintaining this mutation than does introgression. Our results show how suppressed recombination and large-scale mutation can help package gene complexes into discrete units of diversity, such as morphs, ecotypes, or species.

opencc-zeroAug 2020View details →

Cryptic sexual dimorphism reveals differing selection pressures on continental islands - Sulawesi Babbler (Pellorneum celebense) Morphometric Dataset

Birds are well known for their sexual dimorphism. But not all forms of dimorphism are the same, and differences in morphology can be so subtle that they aren't detected by casual observation. We report that this is the case with the Sulawesi Babbler (Pellorneum celebense), the first reported instance of sexual dimorphism in this species or any of the ground babblers of the Southeast Asian islands. Our finding is based on a combination of morphometric analyses, genetic sexing, and observation of breeding condition. We highlight the utility of unsupervised clustering approaches, widely used in the biomedical literature, for the investigation of sexual dimorphism in ecological and evolutionary contexts. The sexual dimorphism was weaker on the mainland of Sulawesi and stronger on the continental islands of Kabaena, Muna, and Buton. This suggests that different evolutionary pressures have led the species to partition niches differently in these habitats, which separated only recently in geological history. This kind of intraspecific niche partitioning is an intrinsic part of the ecological niche of such species, one we must not miss if we are to fully understand these endlessly fascinating organisms and systems.

opencc-zeroSep 2020View details →

Cuscuta sect. Californicae (Convolvulaceae) revisited: 'cryptic' speciation and host range differentiation

Cuscuta californica complex (sensu lato, s.l.) is a western North American group of species in which the infrastaminal scales are reduced, making the morphological delimitation of species particularly challenging. A revision of this group was prompted by the discovery of an apparent new species from central California based primarily on molecular means. Prompted by this finding, the morphological limits of C. californica s.l. species were comprehensively re-evaluated through a morphometric study. DNA sequences from plastid (trnL–F region and rbcL), nuclear ribosomal ITS and 26S rDNA, as well as a low-copy nuclear pentatricopeptide repeat (PPR) gene were used to reconstruct evolutionary relationships among taxa. Last but not least, the host range of relevant taxa was determined using herbarium specimens. Molecular results strongly supported the new species, C. difficilis, which was found to be morphologically separated from C. brachycalyx only by subtle calyx lobe and corolla tube shape differences. Despite sharing some of the hosts, all the members of C. californica s.l. exhibited a differentiation of their host ranges. An identification key and description of the new species were provided together with a discussion on the systematics and host range of C. californica s.l.. Hybridization, accompanied by plastid capture, was suggested as a possible mechanism of speciation for C. brachycalyx.

opencc-zeroDec 2020View details →

Identifying diagnostic genetic markers for a cryptic invasive agricultural pest: a test case using the apple maggot fly, Rhagoletis pomonella (Diptera: Tephritidae)

Insect pests destroy ~15% of all USA crops, resulting in losses of $15 billion annually. Thus, developing cheap, quick and reliable methods for detecting harmful species is critical to curtail insect damage and lessen economic impact. The apple maggot fly, Rhagoletis pomonella (Diptera: Tephritidae), is a major invasive pest threatening the multibillion-dollar apple industry in the Pacific Northwest USA. The fly is also sympatric with a benign but morphologically similar and genetically closely related species, R. zephyria, which attacks non-commercial snowberry. Unambiguous species identification is essential due to a zero-infestation policy of apple maggot for fruit export. Mistaking R. zephyria for R. pomonella triggers unnecessary and costly quarantines, diverting valuable control resources. Here we develop and apply a relatively simple and cost-effective diagnostic approach using Illumina sequencing of double digest restriction-site associated DNA markers. We identified five informative single nucleotide polymorphisms (SNPs) and designed a diagnostic test based on agarose gel electrophoresis of restriction enzyme digested polymerase chain reaction amplification products (RFLPs) to distinguish fly species. We demonstrated the utility of this approach for immediate, one day species identification by scoring apple- and snowberry-infesting flies of known host plant identity, reared directly from 11 sites throughout Washington. However, if immediate diagnosis is not required, or hundreds to thousands of specimens must be assessed, then a direct Illumina-based sequencing strategy, similar to that used here for diagnostic SNP identification can be powerful and cost-effective. The genomic strategy we present is effective for R. pomonella and also transferable to many cryptic pests.

opencc-zeroJun 2019View details →

Data from: The effects of heterospecific mating frequency on the strength of cryptic reproductive barriers

Heterospecific mating frequency is critical to hybrid zone dynamics and can directly impact the strength of reproductive barriers and patterns of introgression. The ef‐ fectiveness of post‐mating prezygotic (PMPZ) reproductive barriers, which include reduced fecundity via heterospecific matings and conspecific sperm precedence, may depend on the number, identity and order of mates. Studies of PMPZ barriers suggest that they may be important in many systems, but whether these barriers are effective at realistic heterospecific mating frequencies has not been tested. Here, we evaluate the strength of cryptic reproductive isolation in two leaf beetles (Chrysochus auratus and C. cobaltinus) in the context of a range of heterospecific mating frequen‐ cies observed in natural populations. We found both species benefited from multiple matings, but the benefits were greater in C. cobaltinus and extended to heterospecific matings. We found that PMPZ barriers greatly limited hybrid production by C. aura- tus females with moderate heterospecific mating frequencies, but that their effec‐ tiveness diminished at higher heterospecific mating frequencies. In contrast, there was no evidence for PMPZ barriers in C. cobaltinus females at any heterospecific mating frequency. We show that integrating realistic estimates of cryptic isolation with information on relative abundance and heterospecific mating frequency in the field substantially improves our understanding of the strong directional bias in F1 production previously documented in the Chrysochus hybrid zone. Our results dem‐ onstrate that heterospecific mating frequency is critical to understanding the impact of cryptic post‐copulatory barriers on hybrid zone structure and dynamics, and that future studies of such barriers should incorporate field‐relevant heterospecific mat‐ ing frequencies.

opencc-zeroDec 2017View details →

Data from: Intragenomic nuclear RNA variation in a cryptic Amanita taxon

Amanita cf. lavendula collections in eastern North America, Mexico, and Costa Rica were found to consist of four cryptic taxa, one of which exhibited consistently unreadable nuclear rDNA ITS1-5.8S-ITS2 (fungal barcode) sequences after ITS1 base 130. This taxon is designated here as Amanita cf. lavendula taxon 1. ITS sequences from dikaryotic basidiomata were cloned, but sequences recovered from cloning did not segregate into distinct haplotypes. Rather, there was a mix of haplotypes that varied among themselves predominantly at 28 ITS positions. Analysis of each of these 28 variable bases showed predominantly two alternate bases at each position. Based on these findings and additional sequence data from the nuclear rDNA 28S, RNA polymerase II subunit 2 (RPB2) and mitochondrial rDNA small subunit (SSU) and 23S genes, we speculate that taxon 1 represents an initial hybridization event between two divergent taxa followed by failure of the ribosomal repeat to homogenize. Homogenization failure may be a result of repeated hybridization between divergent internal transcribed spacer (ITS) types with inadequate time for concerted evolution of the ribosomal repeat or, alternately, a complete failure of the ribosomal homogenization process. To our knowledge, this finding represents the first report of a geographically widespread taxon (Canada, eastern USA, Costa Rica) with apparent homogenization failure across all collections. Findings such as these have implications for fungal barcoding efforts and the application of fungal barcodes in identifying environmental sequences.

Data from: Embracing discordance: phylogenomic analyses provide evidence for allopolyploidy leading to cryptic diversity in a Mediterranean Campanula (Campanulaceae) clade

The Mediterranean Basin harbors a remarkable amount of biodiversity, a high proportion of which is endemic to this region. Here, we present an in-depth study of an angiosperm species complex, in which cryptic taxonomic diversity has been hypothesized. Specifically, we focus on four currently recognized species in the Roucela complex, a well-supported clade in the Campanulaceae/Campanuloideae: Campanula creutzburgii, C. drabifolia, C. erinus, and C. simulans. This study takes a phylogenomic approach, utilizing near-complete plastomes and 130 nuclear loci, to uncover cryptic diversity and test hypotheses regarding hybridization and polyploidy within this clade. Genome size estimates recovered tetraploid and octoploid lineages within the currently recognized, widespread species C. erinus, showing an east-west geographic pattern. Though genomic data clearly differentiate these two cytotypes, we failed to discern morphological differences. The formation of a cryptic octoploid lineage, distributed across the eastern Mediterranean, is hypothesized to be the result of an allopolyploid event in which one parental morphology is retained. The tetraploid C. erinus and C. creutzburgii (also a tetraploid) are implicated as parental lineages. Our results highlight the utility of target-enrichment approaches for obtaining genomic datasets for thorough assessments of species diversity and the importance of carefully considering gene-tree discordance within such datasets.

opencc-zeroDec 2017View details →

Data from: Breeding season length and nest mortality drive cryptic life history variation in Dark-eyed Juncos (Junco hyemalis) breeding across a montane elevation gradient

The manner in which individual life history traits respond to the environment and to each other, and how these traits combine to form overall patterns of life history variation, remains poorly characterized in wild populations. We monitored breeding Dark-eyed Juncos (Junco hyemalis) across a 700-m elevational range. We compared breeding season length, temporal patterns of breeding activity, adult body size, clutch size, brood size, nestling quality, and nest mortality among elevations. We also compared environmental measures across the studied elevations to determine whether abiotic factors explained life history trait variation. We used 12 microsatellite loci to test for genetic differentiation in populations at different elevations. Finally, we constructed a computer simulation to evaluate the combined effects of observed variation in life history traits. We found differences among elevations in breeding season length and in patterns of reproductive timing, which did not match each other and which were not explained solely by abiotic factors. We found no differences among elevations in adult body size, clutch size, brood size, or nestling quality. Nest mortality increased significantly with elevation. Genetic differentiation was too low to define distinct subpopulations. The simulation suggested that differences in mortality, in combination with differences in breeding season length, contributed to substantial differences in reproductive success among elevations. Thus, although individual life history traits showed little evidence of variation in response to the environment or to each other and little genetic differentiation, variation in breeding season length and in nest mortality were potential drivers of substantial elevational variation in overall life history in this system. These results demonstrate that individual life history traits may vary substantially in their patterns of variation, and that some life history traits may have disproportionate effects on overall life history.

opencc-zeroDec 2018View details →

Data from: Dense geographic and genomic sampling reveals paraphyly and a cryptic lineage in a classic sibling species complex

Incomplete or geographically biased sampling poses significant problems for research in phylogeography, population genetics, phylogenetics, and species delimitation. Despite the power of using genome-wide genetic markers in systematics and related fields, approaches such as the multispecies coalescent remain unable to easily account for unsampled lineages. The Empidonax difficilis / E. occidentalis complex of small tyrannid flycatchers (Aves: Tyrannidae) is a classic example of widely-distributed species with limited phenotypic geographic variation that was broken into two largely cryptic (or "sibling") lineages following extensive study. Though the group is well-characterized north of the U.S. Mexico border, the evolutionary distinctiveness and phylogenetic relationships of southern populations remain obscure. In this paper, we use dense genomic and geographic sampling across the majority of the range of the E. difficilis / E . occidentalis complex to assess whether current taxonomy and species limits reflect underlying evolutionary patterns, or whether they are an artifact of historically biased or incomplete sampling. We find that additional samples from Mexico render the widely recognized species-level lineage E. occidentalis paraphyletic, though it retains support in the best-fit species delimitation model from clustering analyses. We further identify a highly divergent unrecognized lineage in a previously unsampled portion of the group's range, which a cline analysis suggests is more reproductively isolated than the currently recognized species E. difficilis and E. occidentalis. Our phylogeny supports a southern origin of these taxa. Our results highlight the pervasive impacts of biased geographic sampling, even in well-studied vertebrate groups like birds, and illustrate what is a common problem when attempting to define species in the face of recent divergence and reticulate evolution.

Data from: Mating patterns and post-mating isolation in three cryptic species of the Engystomops petersi species complex

Determining the extent of reproductive isolation in cryptic species with dynamic geographic ranges can give us important insights into the processes that generate and maintain genetic divergence in the absence of severe geographic barriers. We studied mating patterns, propensity to crossbreed in nature and subsequent fertilization rates, as well as survival and development of hybrid F1 offspring for three species of the E. petersi species complex in Yasuní National Park, Ecuador. We found at least two species in five out of seven locations sampled, and 14.3% of the wild pairs genotyped were heterospecific crosses. We also found reduced fertilization rates in hybrid crosses between E. petersi females and E. "magnus" males, and between E. "magnus" females and E. "selva" males but not in the opposite hybrid crosses, suggesting asymmetric reproductive isolation for these species. Larval development time decreased in F1 hybrid crosses compared to conspecific F1s, but we did not find any reduction in larval survival or early metamorph survival. Our results show evidence of post-mating isolation for at least two hybrid crosses of the cryptic species we studied. The general decrease in fertilization rates in heterospecific crosses suggests that sexual selection and reinforcement might have not only contributed to the pattern of call variation and behavioral isolation we see between species today, but they may also contribute to further signal divergence and behavioral evolution, especially in locations where hybridization is common and fertilization success is diminished.

Data from: Diet reveals links between morphology and foraging in a cryptic temperate reef fish

Predators select prey so as to maximize energy and minimize manipulation time. In order to reduce prey detection and handling time, individuals must actively select their foraging space (microhabitat) and populations exhibit morphologies that are best suited for capturing locally available prey. We explored how variation in diet correlates with habitat type, and how these factors influence key morphological structures (mouth gape, eye diameter, fin length, fin area, and pectoral fin ratio) in a common microcarnivorous cryptic reef fish species, the triplefin Helcogrammoides cunninghami. In a mensurative experiment carried out at six kelp-dominated sites, we observed considerable differences in diet along 400 km of the Chilean coast coincident with variation in habitat availability and prey distributions. Triplefins preferred a single prey type (bivalves or barnacles) at northern sites, coincident with a low diversity of foraging habitats. In contrast, southern sites presented varied and heterogeneous habitats, where triplefin diets were more diverse and included amphipods, decapods, and cumaceans. Allometry-corrected results indicated that some morphological structures were consistently correlated with different prey items. Specifically, large mouth gape was associated with the capture of highly mobile prey such as decapods, while small mouth gape was more associated with cumaceans and copepods. In contrast, triplefins that capture sessile prey such as hydroids tend to have larger eyes. Therefore, morphological structures co-vary with habitat selection and prey usage in this species. Our study shows how an abundant generalist reef fish exhibits variable feeding morphologies in response to the distribution of potential habitats and prey throughout its range.

Data from: Cryptic species in the mountaintops: species delimitation and taxonomy of the Bembidion breve species group (Coleoptera: Carabidae) aided by genomic architecture of a century-old type specimen

The breve species group includes closely related Bembidion Latreille ground beetles commonly found at high elevation in the mountains of western North America. For several decades, the group has been considered to consist of two species. Here, we present evidence from morphological, molecular and geographic data that the group contains nine species: Bembidion ampliatum, B. breve, B. geopearlis, B. laxatum, B. lividulum, B. oromaia, B. saturatum, B. testatum and B. vulcanix. We describe three species (B. geopearlis, B. oromaia and B. vulcanix) as new and resurrect four previously synonymized names (B. ampliatum, B. lividulum, B. saturatum and B. testatum). Species diversity is highest throughout the Cascades in Oregon and Washington, and Sierra Nevada of California, where up to seven species can occur in sympatry. We resolved challenging nomenclatural issues through analysis of sequences obtained from century-old type specimens by using a novel application of rDNA copy number analysis – an approach that may prove useful for other historical specimens.