Estimating phylogenetic relationships despite discordant gene trees across loci: the species tree of a diverse species group of feather mites (Acari: Proctophyllodidae)

Sequence characteristics, genetic diversity and phylogenetic analysis of the Cucurbita ficifolia (Cucurbitaceae) chloroplasts genome

BACKGROUND

Curcubita ficifolia Bouché (Cucurbitaceae) has high value as a food crop and medicinal plant, and also has horticultural value as rootstock for other melon species. China is home to many different cultivars, but the genetic diversity of these resources and the evolutionary relationships among them, as well as the differences between C. ficifolia and other Cucurbita species, remain unclear.

RESULTS

We investigated the chloroplast (cp) genomes of 160 C. ficifolia individuals from 31 populations in Yunnan, a major C. ficifolia production area in China. We found that the cp genome of C. ficifolia is ~151 kb and contains 128 genes, of which 86 are protein coding genes, 34 encode tRNA, and eight encode rRNAs. We also identified 64 SSRs, mainly AT repeats. The cp genome was found to contain a total of 204 SNP and 57 indels, and a total of 21 haplotypes were found in the 160 study individuals. The reverse repeat (IR) region of C. ficifolia contained a few differences compared with this region in the six other Cucurbita species. Sequence difference analysis demonstrated that most of the variable regions were concentrated in the single copy (SC) region. Moreover, the sequences of the coding regions were found to be more similar among species than those of the non-coding regions. The phylogenies reconstructed from the cp genomes of 61 representative species of Cucurbitaceae reflected the currently accepted classification, in which C. ficifolia is sister to the other Cucurbita species, however, different interspecific relationships were found between Cucurbita species.

CONCLUSIONS

These results will be valuable in the classification of C. ficifolia genetic resources and will contribute to our understanding of evolutionary relationships within the genus Cucurbita.

A new feather mite species of the genus Mycterialges Gaud & Atyeo, 1981 (Acari, Xolalgidae) from the Oriental Stork, Ciconiaboyciana (Ciconiiformes, Ciconiidae) in Korea

A new feather mite species, Mycterialgesboycianaesp. nov. (Xolalgidae), was identified from the Oriental Stork, Ciconiaboyciana Swinhoe, 1873, in Korea. Males of M.boycianaesp. nov. are distinguished from Mycterialgesmesomorphus Gaud & Atyeo, 1981, in having a single triangular prodorsal shield, sinuous margins of the opisthosoma located between setae e2 and h2 on the hysteronotal shield, an oval-shaped epiandrum without posterior extensions, a shorter tibia + tarsus IV than femoragenu IV, and an absent ambulacral disc of leg IV. Females differ in having a prodorsal shield with a posterior margin that is blunt-angular, and a concave posterior margin of the hysteronotal shield with posterior extensions. This study presents the first record of the feather mite genus Mycterialges in birds of the genus Ciconia (Ciconiidae). Additionally, we determined the phylogenetic relationship among Ingrassiinae using the mitochondrial cytochrome c oxidase subunit (COI).

Dispersal-Limited Symbionts Exhibit Unexpectedly Wide Variation in Host Specificity

A fundamental aspect of symbiotic relationships is host specificity, ranging from extreme specialists associated with only a single host species to generalists associated with many different species. Although symbionts with limited dispersal capabilities are expected to be host specialists, some are able to associate with multiple hosts. Understanding the micro- and macro-evolutionary causes of variations in host specificity is often hindered by sampling biases and the limited power of traditional evolutionary markers. Here, we studied feather mites to address the barriers associated with estimates of host specificity for dispersal-limited symbionts. We sampled feather mites (Proctophyllodidae) from a nearly comprehensive set of North American breeding warblers (Parulidae) to study mite phylogenetic relationships and host-symbiont codiversification. We used pooled-sequencing (Pool-Seq) and short-read Illumina technology to interpret results derived from a traditional barcoding gene (cytochrome c oxidase subunit 1) versus 11 protein-coding mitochondrial genes using concatenated and multispecies coalescent approaches. Despite the statistically significant congruence between mite and host phylogenies, mite-host specificity varies widely, and host switching is common regardless of the genetic marker resolution (i.e., barcode vs. multilocus). However, the multilocus approach was more effective than the single barcode in detecting the presence of a heterogeneous Pool-Seq sample. These results suggest that presumed symbiont dispersal capabilities are not always strong indicators of host specificity or of historical host-symbiont coevolutionary events. A comprehensive sampling at fine phylogenetic scales may help to better elucidate the microevolutionary filters that impact macroevolutionary processes regulating symbioses, particularly for dispersal-limited symbionts. [Codiversification; cophylogenetics; feather mites; host switching; pooled sequencing; species delineation; symbiosis, warblers.].

Cox1 barcoding versus multilocus species delimitation: validation of two mite species with contrasting effective population sizes

BACKGROUND

The cox1-barcoding approach is currently extensively used for high-throughput species delimitation and discovery. However, this method has several limitations, particularly when organisms have large effective population sizes. Paradoxically, most common, abundant, and widely distributed species may be misclassified by this technique.

RESULTS

We conducted species delimitation analyses for two host-specific lineages of scab mites of the genus Caparinia, having small population sizes. Cox1 divergence between these lineages was high (7.4-7.8%) while that of nuclear genes was low (0.06-0.53%). This system was contrasted with the medically important American house dust mite, Dermatophagoides farinae, a globally distributed species with very large population size. This species has two distinct, sympatric cox1 lineages with 4.2% divergence. We tested several species delimitation algorithms PTP, GMYC, ABGD, BPP, STACEY and PHRAPL, which inferred different species boundaries for these entities. Notably, STACEY recovered the Caparinia lineages as two species and D. farinae as a single species. BPP agreed with these results when the prior on ancestral effective population sizes was set to expected values, although delimitation of Caparinia was still equivocal. No other cox1 species delimitation algorithms inferred D. farinae as a single species, despite the fact that the nuclear CPW2 gene shows some evidence for introgression between the cox1 groups. This indicates that the cox1-barcoding approach may result in excessive species splitting.

CONCLUSIONS

Our research highlights the importance of using nuclear genes and demographic characteristics to infer species boundaries rather than relying on a single-gene barcoding approach, particularly for putative species having large effective population sizes.

Evolutionary and domestication history of Cucurbita (pumpkin and squash) species inferred from 44 nuclear loci

Phylogenetics can facilitate the study of plant domestication by resolving sister relationships between crops and their wild relatives, thereby identifying the ancestors of cultivated plants. Previous phylogenetic studies of the six Cucurbita crop lineages (pumpkins and squashes) and their wild relatives suggest histories of deep coalescence that complicate uncovering the genetic origins of the six crop taxa. We investigated the evolution of wild and domesticated Cucurbita using the most comprehensive and robust molecular-based phylogeny for Cucurbita to date based on 44 loci derived from introns of single-copy nuclear genes. We discovered novel relationships among Cucurbita species and recovered the first Cucurbita tree with well-supported resolution within species. Cucurbita comprises a clade of mesophytic annual species that includes all six crop taxa and a grade of xerophytic perennial species that represent the ancestral xerophytic habit of the genus. Based on phylogenetic resolution within-species we hypothesize that the magnitude of domestication bottlenecks varies among Cucurbita crop lineages. Our phylogeny clarifies how wild Cucurbita species are related to the domesticated taxa. We find close relationships between two wild species and crop lineages not previously identified. Expanded geographic sampling of key wild species is needed for improved understanding of the evolution of domesticated Cucurbita.

Ectoparasites of the black-chinned siskin Spinus barbatus (Passeriformes: Fringillidae) in Chile

Despite being a bird with a broad and extensive distribution in Chile, the black-chinned siskin, Spinus barbatus Molina, 1782 is not well studied in relation to its parasites. This paper aims to describe the ectoparasite fauna of S. barbatus in central and southern Chile. A total of 125 individuals caught with mist nets were examined alive; a total of 22 parasites were found dead and were exposed to parasit autopsy. The extracted parasites were preserved in 70% alcohol for subsequent mounting and identification. Ectoparasites were found in 56 black-chinned siskins (38%); 48 of them (33%) had 870 mites - 680 feather mites (Astigmata: Analgoidea) were identified as Proctophyllodes spini, 167 as Knemidokoptes jamaicensis, 19 as Strelkoviacarus critesi, and one as Analges passerinus. Moreover, three mites were chiggers belonging to the tribe Schoengastiini (Prostigmata: Trombiculidae). In 21 birds (14%), 54 lice were found, 21 of which were identified as Philopterus roehreri, 18 as Myrsidea serini, and 15 as Ricinus carolynae. Endoparasites were not found in the necropsied individuals. All of the parasites that were found represent new records for Chile, and they also serve as new records of host-parasite associations for S. barbatus.

Advances using molecular data in insect systematics

The size of molecular datasets has been growing exponentially since the mid 1980s, and new technologies have now dramatically increased the slope of this increase. New datasets include genomes, transcriptomes, and hybrid capture data, producing hundreds or thousands of loci. With these datasets, we are approaching a consensus on the higher level insect phylogeny. Huge datasets can produce new challenges in interpreting branch support, and new opportunities in developing better models and more sophisticated partitioning schemes. Dating analyses are improving as we recognize the importance of careful fossil calibration selection. With thousands of genes now available, coalescent methods have come of age. Barcode libraries continue to expand, and new methods are being developed for incorporating them into phylogenies with tens of thousands of individuals.

Phylogenetic position of the house dust mite subfamily Guatemalichinae (Acariformes: Pyroglyphidae) based on integrated molecular and morphological analyses and different measures of support

Based on multilocus phylogenetic analyses (18S, 28S, EF1-α, SRP54, HSP70, CO1, 10 860 nt aligned), we show that the house dust mite subfamily Guatemalichinae is nested within non-onychalgine pyroglyphid mites and forms the sister group to the genus Sturnophagoides (bootstrap support 100, posterior probability 1.0). Because high bootstrap support values may be misleading in the presence of incongruence, we evaluate robustness of the Guatemalichinae+Sturnophagoides clade using: (1) internode certainty indices to estimate the frequency of conflicting bipartitions in maximum-likelihood bootstrap trees, (ii) consensus networks to investigate conflict among different loci; and (iii) statistical hypothesis testing based on information theory, both multi-scale and regular bootstrap. Results suggest that this grouping is very well supported given the data. The molecular analyses were integrated with detailed morphological study using scanning electron and light microscopy. We suggest that the subfamilial status of Guatemalichinae should be reconsidered, and this lineage should be placed within the subfamily Dermatophagoidinae. The latter subfamily is currently accepted in the literature as a monophyletic group but was here inferred as paraphyletic and was not supported by any morphological synapomorphy. The paraphyly involved the most species-rich and medically important genus, Dermatophagoides. Our findings suggest the need for a comprehensive revision of the higher-level relationships of pyroglyphid house dust mites using both DNA sequences and morphology coupled with a broad taxonomic sampling.

Species mtDNA genetic diversity explained by infrapopulation size in a host-symbiont system

Understanding what shapes variation in genetic diversity among species remains a major challenge in evolutionary ecology, and it has been seldom studied in parasites and other host‐symbiont systems. Here, we studied mtDNA variation in a host‐symbiont non‐model system: 418 individual feather mites from 17 feather mite species living on 17 different passerine bird species. We explored how a surrogate of census size, the median infrapopulation size (i.e., the median number of individual parasites per infected host individual), explains mtDNA genetic diversity. Feather mite species genetic diversity was positively correlated with mean infrapopulation size, explaining 34% of the variation. As expected from the biology of feather mites, we found bottleneck signatures for most of the species studied but, in particular, three species presented extremely low mtDNA diversity values given their infrapopulation size. Their star‐like haplotype networks (in contrast with more reticulated networks for the other species) suggested that their low genetic diversity was the consequence of severe bottlenecks or selective sweeps. Our study shows for the first time that mtDNA diversity can be explained by infrapopulation sizes, and suggests that departures from this relationship could be informative of underlying ecological and evolutionary processes.

Origin and higher-level diversification of acariform mites - evidence from nuclear ribosomal genes, extensive taxon sampling, and secondary structure alignment

BACKGROUND

Acariformes is the most species-rich and morphologically diverse radiation of chelicerate arthropods, known from the oldest terrestrial ecosystems. It is also a key lineage in understanding the evolution of this group, with the most vexing question whether mites, or Acari (Parasitiformes and Acariformes) is monophyletic. Previous molecular studies recovered Acari either as monophyletic or non-monophyletic, albeit with a limited taxon sampling. Similarly, relationships between basal acariform groups (include little-known, deep-soil 'endeostigmatan' mites) and major lineages of Acariformes (Sarcoptiformes, Prostigmata) are virtually unknown. We infer phylogeny of chelicerate arthropods, using a large and representative dataset, comprising all main in- and outgroups (228 taxa). Basal diversity of Acariformes is particularly well sampled. With this dataset, we conduct a series of phylogenetically explicit tests of chelicerate and acariform relationships and present a phylogenetic framework for internal relationships of acariform mites.

RESULTS

Our molecular data strongly support a diphyletic Acari, with Acariformes as the sister group to Solifugae (PP =1.0; BP = 100), the so called Poecilophysidea. Among Acariformes, some representatives of the basal group Endeostigmata (mainly deep-soil mites) were recovered as sister-groups to the remaining Acariformes (i. e., Trombidiformes + and most of Sarcoptiformes). Desmonomatan oribatid mites (soil and litter mites) were recovered as the monophyletic sister group of Astigmata (e. g., stored product mites, house dust mites, mange mites, feather and fur mites). Trombidiformes (Sphaerolichida + Prostigmata) is strongly supported (PP =1.0; BP = 98-100). Labidostommatina was inferred as the basal lineage of Prostigmata. Eleutherengona (e. g., spider mites) and Parasitengona (e. g., chiggers, fresh water mites) were recovered as monophyletic. By contrast, Eupodina (e. g., snout mites and relatives) was not. Marine mites (Halacaridae) were traditionally regarded as the sister-group to Bdelloidea (Eupodina), but our analyses show their close relationships to Parasitengona.

CONCLUSIONS

Non-trivial relationships recovered by our analyses with high support (i.e., basal arrangement of endeostigmatid lineages, the position of marine mites, polyphyly of Eupodina) had been proposed by previous underappreciated morphological studies. Thus, we update currently the accepted taxonomic classification to reflect these results: the superfamily Halacaroidea Murray, 1877 is moved from the infraorder Eupodina Krantz, 1978 to Anystina van der Hammen, 1972; and the subfamily Erythracarinae Oudemans, 1936 (formerly in Anystidae Oudemans, 1902) is elevated to family rank, Erythracaridae stat. ressur., leaving Anystidae only with the nominal subfamily. Our study also shows that a clade comprising early derivative Endeostigmata (Alycidae, Nanorchestidae, Nematalycidae, and maybe Alicorhagiidae) should be treated as a taxon with the same rank as Sarcoptiformes and Trombidiformes, and the scope of the superfamily Bdelloidea should be changed. Before turning those findings into nomenclatural changes, however, we consider that our study calls for (i) finding shared apomorphies of the early derivative Endeostigmata clade and the clade including the remaining Acariformes; (ii) a well-supported hypothesis for Alicorhagiidae placement; (iii) sampling the families Proterorhagiidae, Proteonematalycidae and Grandjeanicidae not yet included in molecular analyses; (iv) undertake a denser sampling of clades traditionally placed in Eupodina, Anystina (Trombidiformes) and Palaeosomata (Sarcoptiformes), since consensus networks and Internode certainty (IC) and IC All (ICA) indices indicate high levels of conflict in these tree regions. Our study shows that regions of ambiguous alignment may provide useful phylogenetic signal when secondary structure information is used to guide the alignment procedure and provides an R implementation to the Bayesian Relative Rates test.

Integrated Bayesian species delimitation and morphological diagnostics of chorioptic mange mites (Acariformes: Psoroptidae: Chorioptes)

The external morphology of adult and immature stages of mange mites of the genus Chorioptes was investigated with the aid of light and scanning electron microscopy. A molecular phylogeny of this genus was inferred based on six genes (18S, 28S rDNA, EF1-α, SRP54, HSP70, and CO1). The validity of four species (Ch. bovis, Ch. panda, Ch. texanus, and Ch. sweatmani sp. nov. described from the moose from Sweden, Finland, and Russia) was confirmed based on morphology and a Bayesian species delimitation analysis incorporating both gene tree uncertainties and incomplete lineage sorting via the coalescent process model in BPP. Sequence data for Ch. crewei and Ch. mydaus was not available but their morphology strongly suggests their validity. The six valid Chorioptes species are diagnosed using type and non-type specimens, and a key to species is provided. Ch. sweatmani differs from closely related Ch. texanus by the following features: in males, the body length, including the gnathosoma, is 380-405 μm (vs. 220-295 in Ch. texanus), the idiosoma is 3-4 times longer than setae cp (vs. 1.3-1.6 times longer), legs III are approximately three times longer than setae sRIII (vs. 1.8-2 times longer), the apical spur of tarsus III is curved (vs. straight), a spur near seta fIII base is not developed (vs. small but distinct); in females, setae h2 are 1.4-1.5 times shorter than legs IV (vs. about two times longer). Hosts and distribution records of Chorioptes species are summarized.

Is permanent parasitism reversible?--critical evidence from early evolution of house dust mites

Long-term specialization may limit the ability of a species to respond to new environmental conditions and lead to a higher likelihood of extinction. For permanent parasites and other symbionts, the most intriguing question is whether these organisms can return to a free-living lifestyle and, thus, escape an evolutionary "dead end." This question is directly related to Dollo's law, which stipulates that a complex trait (such as being free living vs. parasitic) cannot re-evolve again in the same form. Here, we present conclusive evidence that house dust mites, a group of medically important free-living organisms, evolved from permanent parasites of warm-blooded vertebrates. A robust, multigene topology (315 taxa, 8942 nt), ancestral character state reconstruction, and a test for irreversible evolution (Dollo's law) demonstrate that house dust mites have abandoned a parasitic lifestyle, secondarily becoming free living, and then speciated in several habitats. Hence, as exemplified by this model system, highly specialized permanent parasites may drastically de-specialize to the extent of becoming free living and, thus escape from dead-end evolution. Our phylogenetic and historical ecological framework explains the limited cross-reactivity between allergens from the house dust mites and "storage" mites and the ability of the dust mites to inhibit host immune responses. It also provides insights into how ancestral features related to parasitism (frequent ancestral shifts to unrelated hosts, tolerance to lower humidity, and pre-existing enzymes targeting skin and keratinous materials) played a major role in reversal to the free-living state. We propose that parasitic ancestors of pyroglyphids shifted to nests of vertebrates. Later the nest-inhabiting pyroglyphids expanded into human dwellings to become a major source of allergens.