Detecting ancient codispersals and host shifts by double dating of host and parasite phylogenies: Application in proctophyllodid feather mites associated with passerine birds

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).

Horizontal transmission maintains host specificity and codiversification of symbionts in a brood parasitic host

In host-symbiont systems, interspecific transmissions create opportunities for host switches, potentially leading to cophylogenetic incongruence. In contrast, conspecific transmissions often result in high host specificity and congruent cophylogenies. In most bird-feather mite systems, conspecific transmission is considered dominant, while interspecific transmission is supposedly rare. However, while mites typically maintain high host specificity, incongruent cophylogenies are common. To explain this conundrum, we quantify the magnitude of conspecific vs. interspecific transmission in the brood parasitic shiny cowbird (Molothrus bonariensis). M. bonariensis lacks parental care, allowing the assessment of the role of horizontal transmission alone in maintaining host specificity. We found that despite frequent interspecific interactions via foster parental care, mite species dispersing via conspecific horizontal contacts are three times more likely to colonize M. bonariensis than mites transmitted vertically via foster parents. The results highlight the previously underappreciated rate of transmission via horizontal contacts in maintaining host specificity on a microevolutionary scale. On a macroevolutionary scale, however, host switches were estimated to have occurred as frequently as codivergences. This suggests that macroevolutionary patterns resulting from rare events cannot be easily generalized from short-term evolutionary trends.

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.].

Two new species of feather mites (Acariformes, Astigmata) from the black-tailed godwit, Limosa limosa (Charadriiformes, Scolopacidae), in Korea

Two new species of feather mites are described from two individuals of the black-tailed godwit, Limosa limosa (Linnaeus, 1758), in Korea: Alloptes (Conuralloptes) neolimosaesp. nov. (Analgoidea, Alloptidae) and Phyllochaeta limosaesp. nov. (Pterolichoidea, Syringobiidae). Males of A. (C.) neolimosaesp. nov. are distinguished from A. (C.) limosae in having the hysteronotal shield with a straight anterior margin, setae h2 enlarged and slightly flattened in the basal half, and the terminal lamella monotonously transparent without sclerotized patches; females differ in having legs IV with ambulacral discs extending to or slightly beyond the level of setae f2. The discovery of P. limosaesp. nov. represents the first record of the feather mite genus Phyllochaeta on godwits of the genus Limosa Brisson, 1760 (Scolopacidae, Limosinae). Males of P. limosaesp. nov. are distinguished from P. secunda in having the terminal cleft semi-ovoid with a length-to-width ratio of 1.7, and the terminal membranes with 15 or 16 finger-shaped denticles; females differ in having the hysteronotal shield bearing faint longitudinal striations in the posterior third and lacking lacunae, and setae c1 situated posterior to the level of setae c2. Additionally, we obtained partial sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene from A. (C.) neolimosaesp. nov. and estimated genetic distances from 10 other Alloptes species based on comparisons of COI sequences.

The evolution, ecology, and conservation of hummingbirds and their interactions with flowering plants

The ecological co-dependency between plants and hummingbirds is a classic example of a mutualistic interaction: hummingbirds rely on floral nectar to fuel their rapid metabolisms, and more than 7000 plant species rely on hummingbirds for pollination. However, threats to hummingbirds are mounting, with 10% of 366 species considered globally threatened and 60% in decline. Despite the important ecological implications of these population declines, no recent review has examined plant-hummingbird interactions in the wider context of their evolution, ecology, and conservation. To provide this overview, we (i) assess the extent to which plants and hummingbirds have coevolved over millions of years, (ii) examine the mechanisms underlying plant-hummingbird interaction frequencies and hummingbird specialization, (iii) explore the factors driving the decline of hummingbird populations, and (iv) map out directions for future research and conservation. We find that, despite close associations between plants and hummingbirds, acquiring evidence for coevolution (versus one-sided adaptation) is difficult because data on fitness outcomes for both partners are required. Thus, linking plant-hummingbird interactions to plant reproduction is not only a major avenue for future coevolutionary work, but also for studies of interaction networks, which rarely incorporate pollinator effectiveness. Nevertheless, over the past decade, a growing body of literature on plant-hummingbird networks suggests that hummingbirds form relationships with plants primarily based on overlapping phenologies and trait-matching between bill length and flower length. On the other hand, species-level specialization appears to depend primarily on local community context, such as hummingbird abundance and nectar availability. Finally, although hummingbirds are commonly viewed as resilient opportunists that thrive in brushy habitats, we find that range size and forest dependency are key predictors of hummingbird extinction risk. A critical direction for future research is to examine how potential stressors - such as habitat loss and fragmentation, climate change, and introduction of non-native plants - may interact to affect hummingbirds and the plants they pollinate.

The explosive radiation, intense host-shifts and long-term failure to speciate in the evolutionary history of the feather mite genus Analges (Acariformes: Analgidae) from European passerines

Mites of the genus Analges (Acariformes: Analgidae) inhabit the down feathers of passeriform birds. The evolutionary history of Analges and the co-phylogentic relationships between these mites and their hosts are unknown. Our phylogenetic analysis supported the monophyly of the genus, but it did not support previous taxonomic hypotheses subdividing the genus into the subgenera Analges and Analgopsis or arranging some species into the A. chelopus and A. passerinus species groups. Molecular data reveal seven new species inhabiting Eurasian passerines and support the existence of several multi-host species. According to molecular dating, the origin of the Analges (c. 41 Mya) coincided with the Eocene diversification of Passerida into Sylvioidea and Muscicapoidea–Passeroidea. The initial diversification of Analges took place on the Muscicapoidea clade, while remaining passerine superfamilies appear to have been colonized because of host-switching. Co-speciation appears to be relatively common among Analges species and their hosts, but the most striking pattern in the co-phylogenetic scenario involves numerous complete host-switches, spreads and several failures to speciate. The mechanism of long-term gene-flow among different populations of multi-host Analges species is enigmatic and difficult to resolve. Probably, in some cases mites could be transferred between birds via feathers used as nest material.

Cophylogenetic analyses of Trachymyrmex ant-fungal specificity: "One to one with some exceptions"

Over the past few decades, large-scale phylogenetic analyses of fungus-gardening ants and their symbiotic fungi have depicted strong concordance among major clades of ants and their symbiotic fungi, yet within clades, fungus sharing is widespread among unrelated ant lineages. Sharing has been explained using a diffuse coevolution model within major clades. Understanding horizontal exchange within clades has been limited by conventional genetic markers that lack both interspecific and geographic variation. To examine whether reports of horizontal exchange were indeed due to symbiont sharing or the result of employing relatively uninformative molecular markers, samples of Trachymyrmex arizonensis and Trachymyrmex pomonae and their fungi were collected from native populations in Arizona and genotyped using conventional marker genes and genome-wide single nucleotide polymorphisms (SNPs). Conventional markers of the fungal symbionts generally exhibited cophylogenetic patterns that were consistent with some symbiont sharing, but most fungal clades had low support. SNP analysis, in contrast, indicated that each ant species exhibited fidelity to its own fungal subclade with only one instance of a colony growing a fungus that was otherwise associated with a different ant species. This evidence supports a pattern of codivergence between Trachymyrmex species and their fungi, and thus a diffuse coevolutionary model may not accurately predict symbiont exchange. These results suggest that fungal sharing across host species in these symbioses may be less extensive than previously thought.

Sharing a bed with mites: preferences of the house dust mite Dermatophagoides farinae in a temperature gradient

House dust mites inhabit bed mattresses contaminating them with allergens. A strong temperature/moisture gradient exists in mattresses when it is used by humans daily. Here, we studied migration patterns of the mite Dermatophagoides farinae in continuous and time-discontinuous temperature gradients consisting of five sectors with 19-23, 23-28, 28-32, 32-36 and 36-41 °C, containing dye-labeled diets as an indicator of mite presence and feeding. The mites migrated through the sectors and fed on the labeled diets or stayed unfed. The numbers of mites with the same coloration in their guts and the numbers of unfed mites in the sectors were recorded. Unfed mites provided information on short-term temperature preferences. Apart from a control trial, two experiments were performed: (i) a constant 19-41 °C gradient for 24 h, and (ii) alternating cycles of the same temperature gradient (19-41 °C, 8 h) and room temperature (16 h) for 5 days to model the typical daily occupancy of bed by humans. In both experiments, fed mites preferred a sector with 32-36 °C, suggesting that in mattresses, house dust mites prefer to stay as close as possible to the resting human, thus maximizing allergen exposure. However, the number of unfed mites decreased with increased temperatures in the gradient. Experiment (ii) showed that the fed mites remained at the same optimal distance from the heat source, suggesting that they stay at the upper surface of the regularly used mattress, even when human was temporarily absent during the day. Unfed mites apparently hide deeper in mattresses as suggested by their avoidance of increased temperatures.

Next-generation cophylogeny: unravelling eco-evolutionary processes

A fundamental question in evolutionary biology is how microevolutionary processes translate into species diversification. Cophylogeny provides an appropriate framework to address this for symbiotic associations, but historically has been primarily limited to unveiling patterns. We argue that it is essential to integrate advances from ecology and evolutionary biology into cophylogeny, to gain greater mechanistic insights and transform cophylogeny into a platform to advance understanding of interspecific interactions and diversification more widely. We discuss key directions, such as incorporating trait reconstruction and considering multiple scales of network organization, and highlight recent developments for implementation. A new quantitative framework is proposed to allow integration of relevant information, such as quantitative traits and assessment of the contribution of individual mechanisms to cophylogenetic patterns.

New feather mites of the Nycteridocaulus generic group (Acariformes: Proctophyllodidae) from passerines (Passeriformes) in Panama

Three new feather mite species of the Nycteridocaulus generic group (Proctophyllodidae: Proctophyllodinae) are described from passerines in Panama: Atrichophyllodes myrmotherulae sp. n. from the Slaty Antwren, Myrmotherula schisticolor (Lawrence) (Thamnophilidae), Nycteridocaulus apanaskevichi sp. n. from the Grey-breasted Wood Wren, Henicorhina leucophrys (Tschudi) (Troglodytidae), and N. empidonicus sp. n. from the Yellowish Flycatcher Empidonax flavescens Lawrence (Tyrannidae). Nycteridocaulus apanaskevichi, presenting the second record of the genus from a host of oscine passerines, differs from N. guaratubensis Hernandes, 2014 in having the anterolateral extensions of the prodorsal shield rounded and the hysteronotal shield lacking any ornamentation. Males of N. empidonicus differ from N. myiobius Mironov, 2017 in having the supranal concavity open posteriorly and tarsus IV with rounded apical process; and females are distinguished by macrosetae h2 having long filiform apices. Males of A. myrmotherulae most clearly differ from A. mentalis Hernandes et al. 2007 in having the terminal lamellae rectangular and tarsus IV with triangular ventral process, and females are distinguished in having a noticeably longer idiosoma, 400-430 μm long. Comments on systematics and host associations of the genera Atrichophyllodes and Nycteridocaulus are provided.

Random Tanglegram Partitions (Random TaPas): An Alexandrian Approach to the Cophylogenetic Gordian Knot

Symbiosis is a key driver of evolutionary novelty and ecological diversity, but our understanding of how macroevolutionary processes originate extant symbiotic associations is still very incomplete. Cophylogenetic tools are used to assess the congruence between the phylogenies of two groups of organisms related by extant associations. If phylogenetic congruence is higher than expected by chance, we conclude that there is cophylogenetic signal in the system under study. However, how to quantify cophylogenetic signal is still an open issue. We present a novel approach, Random Tanglegram Partitions (Random TaPas) that applies a given global-fit method to random partial tanglegrams of a fixed size to identify the associations, terminals, and nodes that maximize phylogenetic congruence. By means of simulations, we show that the output value produced is inversely proportional to the number and proportion of cospeciation events employed to build simulated tanglegrams. In addition, with time-calibrated trees, Random TaPas can also distinguish cospeciation from pseudocospeciation. Random TaPas can handle large tanglegrams in affordable computational time and incorporates phylogenetic uncertainty in the analyses. We demonstrate its application with two real examples: passerine birds and their feather mites, and orchids and bee pollinators. In both systems, Random TaPas revealed low cophylogenetic signal, but mapping its variation onto the tanglegram pointed to two different coevolutionary processes. We suggest that the recursive partitioning of the tanglegram buffers the effect of phylogenetic nonindependence occurring in current global-fit methods and therefore Random TaPas is more reliable than regular global-fit methods to identify host-symbiont associations that contribute most to cophylogenetic signal. Random TaPas can be implemented in the public-domain statistical software R with scripts provided herein. A User's Guide is also available at GitHub.[Codiversification; coevolution; cophylogenetic signal; Symbiosis.].

Macroevolutionary dynamics of parasite diversification: A reality check

Parasitism is often invoked as a factor explaining the variation in diversification rates across the tree of life, while also representing up to half of Earth's diversity. Yet, patterns and processes of parasite diversification remain mostly unknown. In this study, we assess the patterns of parasite diversification and specifically determine the role of life-history traits (i.e. life cycle complexity and host range) and major coevolutionary events in driving diversification across eight phylogenetic datasets spanning taxonomically different parasite groups. Aware of the degree of incomplete sampling among all parasite phylogenies, we also tested the impact of sampling bias on estimates of diversification. We show that the patterns and rates of parasite diversification differ among taxa according to life cycle complexity and to some extent major host transitions. Only directly transmitted parasites were found to be influenced by an effect of major host transitions on diversification rates. Although parasitism may be a main factor responsible for heterogeneity in diversification among the tree of life, the high degree of incomplete parasite phylogenies remains an obstacle when modelling diversification dynamics. Nevertheless, we provide the first comparative test of parasite diversification, revealing some consistent patterns and insight into the processes that shape it.

A NEW GENUS OF THE FEATHER MITE FAMILY PROCTOPHYLLODIDAE (ACARIFORMES: ANALGOIDEA) FROM WOODCREEPERS (PASSERIFORMES: FURNARIIDAE: DENDROCOLAPTINAE) IN THE NEOTROPICS

A new feather mite genus Dendrocolaptobius gen. n. belonging to the Nycteridocaulus generic group (Proctophyllodidae: Proctophyllodinae) is described. The genus includes two species associated with woodcreepers (Furnariidae: Dendrocopaptinae): Dendrocolaptobius cuneiformis (Mironov, 2017) comb. n. previously described from Sittasomus griseicapillus (Vieillot) in Costa Rica; and D. lepidocolapti sp. n. described herein from Lepidocolaptes souleyetii (Lafresnaye) in Panama. The new genus Dendrocolaptobius is clearly distinguished from the other genera of the Nycteridocaulus group in having an inverted genital arch and enlarged bow-shaped basal sclerite in males and the copulatory opening situated dorsally on the lobar region in females.

Phylogeny, origin and dispersal of Saussurea (Asteraceae) based on chloroplast genome data

Saussurea is one of the largest genera of the tribe Cardueae of Asteraceae, comprising about 460 species from the Northern Hemisphere with most species distributed in QTPss and adjacent areas. Here, we established a well-supported phylogenetic framework for Saussurea based on whole chloroplast genomes of 136 taxa plus 16 additional taxa of Cardueae using Bayesian inference and Maximum Likelihood. Our phylogenetic results are inconsistent with previous subgeneric classifications of Saussurea. We nearly completely delimited subgen. Eriocoryne, and found that subgen. Theodorea, subgen. Saussurea section Laguranthera and Rosulascentes are closely related to each other. Based on our phylogenetic results, we performed biogeographic analyses and inferred that the genus Saussurea arose during early-middle Miocene within the Hengduan Mountains. We expect that landscape heterogeneity within the QTPss and adjacent areas, such as the Hengduan Mountains, played an important role in the evolution of Saussurea. Following its evolutionary origin, the genus underwent rapid diversification in situs and dispersed northwards in several migrational patterns. Both continuous uplift of the QTPss and adjacent areas as well as global cooling since mid-Miocene probably led to geographic expansion and diffusion of Saussurea, with the latter, in particular, resulting in the northward dispersal.

Unexpected bird-feather mite associations revealed by DNA metabarcoding uncovers a dynamic ecoevolutionary scenario

The high relevance of host-switching for the diversification of highly host-specific symbionts (i.e., those commonly inhabiting a single host species) demands a better understanding of host-switching dynamics at an ecological scale. Here, we used DNA metabarcoding to study feather mites on passerine birds in Spain, sequencing mtDNA (COI) for 25,540 individual mites (representing 64 species) from 1,130 birds (representing 71 species). Surprisingly, 1,228 (4.8%) mites from 84 (7.4%) birds were found on host species that were not the expected to be a host according to a recent bird-feather mite associations catalog. Unexpected associations were widespread across studied mite (40.6%) and bird (43.7%) species and showed smaller average infrapopulation sizes than typical associations. Unexpected mite species colonized hosts being distantly related to the set of their usual hosts, but with similar body size. The network of bird-mite associations was modular (i.e., some groups of bird and mite species tended to be more associated with each other than with the others), with 75.9% of the unexpected associations appearing within the module of the typical hosts of the mite species. Lastly, 68.4% of mite species found on unexpected hosts showed signatures of genetic differentiation, and we found evidence for reproduction or the potential for it in many of the unexpected associations. Results show host colonization as a common phenomenon even for these putatively highly host-specific symbionts. Thus, host-switching by feather mites, rather than a rare phenomenon, appears as a relatively frequent phenomenon shaped by ecological filters such as host morphology and is revealed as a fundamental component for a dynamic coevolutionary and codiversification scenario.

Feather mites play a role in cleaning host feathers: New insights from DNA metabarcoding and microscopy

Parasites and other symbionts are crucial components of ecosystems, regulating host populations and supporting food webs. However, most symbiont systems, especially those involving commensals and mutualists, are relatively poorly understood. In this study, we have investigated the nature of the symbiotic relationship between birds and their most abundant and diverse ectosymbionts: the vane-dwelling feather mites. For this purpose, we studied the diet of feather mites using two complementary methods. First, we used light microscopy to examine the gut contents of 1,300 individual feather mites representing 100 mite genera (18 families) from 190 bird species belonging to 72 families and 19 orders. Second, we used high-throughput sequencing (HTS) and DNA metabarcoding to determine gut contents from 1,833 individual mites of 18 species inhabiting 18 bird species. Results showed fungi and potentially bacteria as the main food resources for feather mites (apart from potential bird uropygial gland oil). Diatoms and plant matter appeared as rare food resources for feather mites. Importantly, we did not find any evidence of feather mites feeding upon bird resources (e.g., blood, skin) other than potentially uropygial gland oil. In addition, we found a high prevalence of both keratinophilic and pathogenic fungal taxa in the feather mite species examined. Altogether, our results shed light on the long-standing question of the nature of the relationship between birds and their vane-dwelling feather mites, supporting previous evidence for a commensalistic-mutualistic role of feather mites, which are revealed as likely fungivore-microbivore-detritivore symbionts of bird feathers.