Adaptation,ancestral variation and gene flow in a ‘Sky Island’ Drosophila species

Over time, populations of species can expand, contract, fragment and become isolated, creating subpopulations that must adapt to local conditions. Understanding how species maintain variation after divergence as well as adapt to these changes in the face of gene flow is of great interest, especially as the current climate crisis has caused range shifts and frequent migrations for many species. Here, we characterize how a mycophageous fly species, Drosophila innubila, came to inhabit and adapt to its current range which includes mountain forests in south‐western USA separated by large expanses of desert. Using population genomic data from more than 300 wild‐caught individuals, we examine four populations to determine their population history in these mountain forests, looking for signatures of local adaptation. In this first extensive study, establishing D. innubila as a key genomic "Sky Island" model, we find D. innubila spread northwards during the previous glaciation period (30–100 KYA) and have recently expanded even further (0.2–2 KYA). D. innubila shows little evidence of population structure, consistent with a recent establishment and genetic variation maintained since before geographic stratification. We also find some signatures of recent selective sweeps in chorion proteins and population differentiation in antifungal immune genes suggesting differences in the environments to which flies are adapting. However, we find little support for long‐term recurrent selection in these genes. In contrast, we find evidence of long‐term recurrent positive selection in immune pathways such as the Toll signalling system and the Toll‐regulated antimicrobial peptides.     

Identification of sawflies and horntails (Hymenoptera, ‘Symphyta’) through DNA barcodes: successes and caveats

The ‘Symphyta’ is a paraphyletic assemblage at the base of the order Hymenoptera, comprising 14 families and about 8750 species. All have phytophagous larvae, except for the Orussidae, which are parasitoids. This study presents and evaluates the results of DNA barcoding of approximately 5360 specimens of ‘Symphyta’, mainly adults, and 4362 sequences covering 1037 species were deemed of suitable quality for inclusion in the analysis. All extant families are represented, except for the Anaxyelidae. The majority of species and specimens are from Europe, but approximately 38% of the species and 13% of the specimens are of non‐European origin. The utility of barcoding for species identification and taxonomy of ‘Symphyta’ is discussed on the basis of examples from each of the included families. A significant level of cryptic species diversity was apparent in many groups. Other attractive applications include the identification of immature stages without the need to rear them, community analyses based on metabarcoding of bulk samples and association of the sexes of adults.     

The geography of speciation in narrow‐range endemics of the ‘Haenydra’ lineage (Coleoptera,Hydraenidae, Hydraena)

Aim We test whether species of western Mediterranean aquatic Coleoptera of the ‘Haenydra’ lineage (Hydraenidae, Hydraena) originated through: (1) successive periods of dispersal and speciation, (2) range fragmentation by random vicariance, or (3) range fragmentation by geographic isolation owing to a general reduction of population density. Location Europe. Methods To discriminate between scenarios we use contrasting predictions of the relationship between phylogenetic and geographic distance. The phylogeny was based on 3 kb of four mitochondrial and two nuclear gene fragments of about half of the known species of ‘Haenydra’, including most western Mediterranean taxa. Divergences were estimated using a molecular clock. The relationship between phylogenetic and geographic distance was tested using bivariate plots, Mantel tests and comparison of the observed phylogeny with the one minimizing geographic distances between species, as measured using Euclidean minimum spanning trees (EMSTs). Results The monophyly of ‘Haenydra’ was strongly supported, although its phylogenetic placement was not resolved. ‘Haenydra’ was estimated to be of late Miocene age, with most species originating during the Pleistocene. In two clades (Hydraena tatii and Hydraena emarginata clades) there was a significant association between geographic and phylogenetic distance, and the reconstructed phylogeny was identical to that obtained through the EMST, demonstrating a strong non‐randomness of the geographic distribution of the species. In two other clades (Hydraena iberica and Hydraena bitruncata clades) there was no association between geographic and phylogenetic distance, and the observed phylogeny was not the one minimizing geographic distances. In one of the clades this seems to be due to a secondary, recent range expansion of one species (H. iberica), which erased the geographic signal of their distributions. Main conclusions We show that it is possible to obtain strong evidence of stasis of the geographic ranges of narrow‐range endemic species through the study of their phylogenetic relationships and current distributions. In at least two of the studied clades, current species seem to have originated through the fragmentation of a more widely distributed species, without further range movements. A process of range expansion and fragmentation may have occurred repeatedly within the ‘Haenydra’ lineage, contributing to the accumulation of narrow‐range endemics in Mediterranean Pleistocene refugia.     

The anatomy of Odobenocetops (Delphinoidea, Mammalia), the walrus-like dolphin from the Pliocene of Peru and its palaeobiological implications

The Pliocene Beds of the Pisco Formation on the southern coast of Peru have yielded three new skulls of the walrus-like odontocete, Odobenocetops (Delphinoidea, Cetacea). Two of the skulls are from a slightly younger horizon than the holotype of O. peruvianus and belong to a different species, O. leptodon . The holotype of O. leptodon bears a 135 cm long needle-like right tusk and a small 25 cm long left tusk, the apex of which was erupted. The third skull, referred to a female of O. peruvianus , bears two small tusks similar in size to the small left tusk of the holotype. The new specimens include periotic, tympanic and ear ossicles, which confirm referral to the Order Cetacea and the morphology of the humerus reinforces affinities of odobenocetopsids to monodontids. Because the anterodorsal edge of its orbit is slightly concave O. leptodon had reduced anterodorsal binocular vision, a condition compensated for by the probable presence of a small melon (and inferred echolocation). The head was bent ventrally when swimming in such a way that the long tusk was approximately parallel to the axis of the body. The extremely salient occipital condyles of Odobenocetops are indicative of great mobility of the neck, probably related to bottom-feeding. © 2002 The Linnean Society of London, Zoological Journal of the Linnean Society , 2002, 134 , 423–452.     

Further evidence of the African antiquity of hyaenodontid (‘Creodonta’, Mammalia) evolution

We report here the new ‘creodont’ Lahimia selloumi gen. et sp. nov. from the late Palaeocene of the Ouled Abdoun Basin (Morocco) as the oldest known Hyaenodontidae with Tinerhodon from the Ouarzazate Basin (Morocco). By contrast to Tinerhodon, Lahimia is unexpectedly derived. Most of its specializations, such as the shortening of the anterior dentition (e.g. loss of P₁) and the talonid reduction and simplification, are strikingly shared with Boualitomus from the Ypresian of the Ouled Abdoun Basin, and are distinctive from other hyaenodontids, including ‘proviverrines’. They are interpreted as synapomorphies evidencing a precociously specialized early African hyaenodontid lineage. Although Lahimia and Boualitomus remain known only by the lower dentition, their relationships with Koholia are suggested by comparison of their molar occlusal pattern. Lahimia and Boualitomus are referred to the Koholiinae, which is representative of an old African endemic lineage, as initially recognized. This remarkable lineage is characterized by synapomorphies of Lahimia and Boualitomus, and also by a shared original prevallum/postvallid shearing. The discovery of Lahimia provides direct evidence for the antiquity of the African evolution of the Hyaenodontidae. This is in agreement with an African origin of the Hyaenodontidae, and with the probable diphyletism of the ‘Creodonta’. Lahimia and the Koholiinae, as well as the diversity of the first Laurasian hyaenodontid lineages, emphasize our poor knowledge of the striking early African hyaenodontid radiation.     

‘After Africa’: the evolutionary history and systematics of the genus Charaxes Ochsenheimer (Lepidoptera: Nymphalidae) in the Indo‐Pacific region

The predominantly Afrotropical genus Charaxes is represented by 31 known species outside of Africa (excluding subgenus Polyura Billberg). We explored the biogeographic history of the genus using every known non‐African species, with several African species as outgroup taxa. A phylogenetic hypothesis is proposed, based on molecular characters of the mitochondrial genes cytochrome oxidase subunit I (COI) and NADH dehydrogenase 5 (ND5), and the nuclear wingless gene. Phylogenetic analyses based on maximum parsimony and Bayesian inference of the combined dataset implies that the Indo‐Pacific Charaxes form a monophyletic assemblage, with the exception of Charaxes solon Fabricius. Eight major lineages are recognized in the Indo‐Pacific, here designated the solon (+African), elwesi, harmodius, amycus, mars, eurialus, latona, nitebis, and bernardus clades. Species group relationships are concordant with morphology and, based on the phylogeny, we present the first systematic appraisal and classification of all non‐African species. A biogeographical analysis reveals that, after the genus originated in Africa, the evolutionary history of Charaxes in the Indo‐Pacific, in particular Wallacea, may be correlated with the inferred geological and climatic history of the region. We propose that Wallacea was the area of origin of all Charaxes (excluding C. solon) occurring to the east of Wallace's [1863] Line. The earliest Indo‐Pacific lineages appear to have diverged subsequent to the initial fragmentation of a palaeo‐continent approximately 13 million years ago. Further diversification in Indo‐Pacific Charaxes appears primarily related to climatic changes during the Pliocene and possibly as recently as the Pleistocene. Although both dispersal and vicariance have played important roles in the evolution of the genus within the region, the latter has been particularly responsible for diversification of Charaxes in Wallacea. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 100 , 457–481.     

The anatomy of a ‘suture zone’ in Amazonian butterflies: a coalescent‐based test for vicariant geographic divergence and speciation

Attempts by biogeographers to understand biotic diversification in the Amazon have often employed contemporary species distribution patterns to support particular theories, such as Pleistocene rainforest refugia, rather than to test among alternative hypotheses. Suture zones, narrow regions where multiple contact zones and hybrid zones between taxa cluster, have been seen as evidence for past expansion of whole biotas that have undergone allopatric divergence in vicariant refuges. We used coalescent analysis of mutilocus sequence data to examine population split times in 22 pairs of geminate taxa in ithomiine and heliconiine butterflies. We test a hypothesis of simultaneous divergence across a suture zone in NE Peru. Our results reveal a scattered time course of diversification in this suture zone, rather than a tight cluster of split times. Additionally, we find rapid diversification within some lineages such as Melinaea contrasting with older divergence within lineages such as the Oleriina (Hyposcada and Oleria). These results strongly reject simple vicariance as a cause of the suture zone. At the same time, observed lineage effects are incompatible with a series of geographically coincident vicariant events which should affect all lineages similarly. Our results suggest that Pleistocene climatic forcing cannot readily explain this Peruvian suture zone. Lineage‐specific biological traits, such as characteristic distances of gene flow or varying rates of parapatric divergence, may be of greater importance.     

Niger Seed (Guizotia abyssinica), a New Host of ‘Candidatus Phytoplasma asteris’ in Iran

Shrubs of niger seed with phyllody and internode elongation symptoms suggestive of phytoplasma infections occurred in the central regions of Iran. Phytoplasma was detected by polymerase chain reaction (PCR) and nested PCR amplifications using phytoplasma universal primer pairs P1/P7 and R16F2n/R16R2. Using aster yellows group–specific primer pair rp(I)F1A/rp(I)R1A, a fragment of 1212 bp of the rp genes was amplified from DNA samples of infected plants. Random fragment length polymorphism (RFLP) analyses of R16F2n/R16R2‐amplified products using the CfoI restriction enzyme confirmed that Iranian niger seed phyllody phytoplasma is associated with aster yellows group phytoplasmas. Sequence analyses of the partial rp genes fragment indicated that the Iranian niger seed phyllody phytoplasma, which was collected from central regions of Iran, is related to ‘Candidatus Phytoplasma asteris’. This is the first report of a phytoplasma infecting the niger seed plant.     

The origin of the animals and a ‘Savannah’ hypothesis for early bilaterian evolution

The earliest evolution of the animals remains a taxing biological problem, as all extant clades are highly derived and the fossil record is not usually considered to be helpful. The rise of the bilaterian animals recorded in the fossil record, commonly known as the ‘Cambrian explosion’, is one of the most significant moments in evolutionary history, and was an event that transformed first marine and then terrestrial environments. We review the phylogeny of early animals and other opisthokonts, and the affinities of the earliest large complex fossils, the so‐called ‘Ediacaran’ taxa. We conclude, based on a variety of lines of evidence, that their affinities most likely lie in various stem groups to large metazoan groupings; a new grouping, the Apoikozoa, is erected to encompass Metazoa and Choanoflagellata. The earliest reasonable fossil evidence for total‐group bilaterians comes from undisputed complex trace fossils that are younger than about 560 Ma, and these diversify greatly as the Ediacaran–Cambrian boundary is crossed a few million years later. It is generally considered that as the bilaterians diversified after this time, their burrowing behaviour destroyed the cyanobacterial mat‐dominated substrates that the enigmatic Ediacaran taxa were associated with, the so‐called ‘Cambrian substrate revolution’, leading to the loss of almost all Ediacara‐aspect diversity in the Cambrian. Why, though, did the energetically expensive and functionally complex burrowing mode of life so typical of later bilaterians arise? Here we propose a much more positive relationship between late‐Ediacaran ecologies and the rise of the bilaterians, with the largely static Ediacaran taxa acting as points of concentration of organic matter both above and below the sediment surface. The breaking of the uniformity of organic carbon availability would have signalled a decisive shift away from the essentially static and monotonous earlier Ediacaran world into the dynamic and burrowing world of the Cambrian. The Ediacaran biota thus played an enabling role in bilaterian evolution similar to that proposed for the Savannah environment for human evolution and bipedality. Rather than being obliterated by the rise of the bilaterians, the subtle remnants of Ediacara‐style taxa within the Cambrian suggest that they remained significant components of Phanerozoic communities, even though at some point their enabling role for bilaterian evolution was presumably taken over by bilaterians or other metazoans. Bilaterian evolution was thus an essentially benthic event that only later impacted the planktonic environment and the style of organic export to the sea floor.     

Predatory behavior and preference of a successful invader, the mud crab Dyspanopeus sayi (Panopeidae), on its bivalve prey

Predator-prey relationships between the panopeid crab, Dyspanopeus sayi, and the mytilid, Musculista senhousia, were investigated. Through laboratory experiments, prey-handling behavior, prey size selection, predator foraging behavior and preferences for two types of prey (M. senhousia and the Manila clam Ruditapes philippinarum) were assessed. Handling time differed significantly with respect to the three prey sizes offered (small: 15.0-20.0 mm shell length, SL; medium: 20.1-25.0 mm SL; and large: 25.1-30.0 mm SL); mud crabs were more efficient in predating medium-small than large prey. Although differences in prey profitability were not evident, D. sayi exhibited a marked reluctance to feed on larger-sized prey whilst smaller, more easily predated mussels were available. Size selection may be the result of a mechanical process in which encountered prey are attacked but rejected if they remain unbroken after a certain number of opening attempts. D. sayi exhibited inverse density-dependent foraging. A significant higher mortality of prey was evident at low prey density. Thus, at low predator density, the D. sayi-M. senhousia interaction was a destabilizing type II functional response. Interference responses affected the magnitude of predation intensity by D. sayi on M. senhousia, since as the density of foraging crabs increased, their foraging success fell. At high density (4 crabs tank⁻¹), crabs engaged in a high amount of agonistic activity when encountering a conspecific specimen, greatly diminished prey mortality. Finally, presenting two types of prey, Manila clam juveniles were poorly predated by mud crabs, which focused their predation mostly on M. senhousia. It is hypothesized that, when more accessible prey is available, mud crabs will have a minimal predatory impact on commercial R. philippinarum juvenile stocks.     

The role of historical factors and natural selection in the evolution of breeding systems of Oxalis alpina in the Sonoran desert ‘Sky Islands’

Pleistocene climatic oscillations are known to influence the patterns of genetic diversity and the distribution of traits that are the target of selection. Here, we combine phylogeographical and ecological niche modelling (ENM) approaches to explore the influence of historical factors (Pleistocene climatic shifts) and natural selection on the evolution of distyly (two floral morphs) from tristyly (three floral morphs) of Oxalis alpina in the Sky Islands of the Sonoran Desert. Molecular data and ENM indicate that historical factors have had a strong influence on the genetic structure and the geographical distribution of reproductive systems of O. alpina. Moreover, genetic results suggest the possibility that distylous populations do not represent a monophyletic group. We propose that the combined effects of natural selection and genetic drift have influenced the tristyly–distyly transition.     

Long‐term ‘islands’ in the landscape: low gene flow,effective population size and genetic divergence in the shrub Hakea oldfieldii (Proteaceae)

The genetic structure of disjunct populations is determined by founding genetic properties, demographic processes, gene flow, drift and local selection. We aim to identify the genetic consequences of natural population disjunction at regional and local scales in Hakea oldfieldii using nuclear and plastid markers to investigate long‐term effective population sizes and gene flow, and patterns of diversity and divergence, among populations. Regional divergence was significant as shown by a consistent pattern in principal coordinates, neighbor‐joining and Bayesian analyses, but divergence at the local level was also significant with localized distribution of plastid haplotypes and populations clustering separately in Bayesian analyses. Historical, recent and first‐generation gene flow was low, suggesting that recent habitat fragmentation has not reduced gene migration significantly. Genetic bottlenecks were detected in three populations. Long‐term effective population size was significantly correlated with the number of alleles/locus and observed heterozygosity, but not with census population size, suggesting that the loss of diversity is associated with long‐term changes rather than recent fragmentation. Inbreeding coefficients were significant in only three populations, suggesting that the loss of diversity is linked to drift and bottlenecks associated with demographic processes (local extinction by fires) rather than inbreeding. Historical disjunction as a result of specific ecological requirements, contraction of habitats following drying during the Pleistocene, low gene flow and changes in population size are likely to have been important forces driving divergence through isolation by distance and drift. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 179 , 319–334.     

Isolation and characterization of microsatellite loci from mother‐of‐millions,Bryophyllum delagoense (Crassulaceae), and its hybrid with Bryophyllum daigremontianum, ‘Houghton's hybrid’

Nine microsatellite loci were developed, and are transferable, across the Madagascan succulents Bryophyllum daigremontianum, Bryophyllum delagoense (mother‐of‐millions) and their horticultural hybrid (Houghton's), from enriched libraries of the later two species. For B. delagoense, a tetraploid, three to 13 alleles per locus were found for native Madagascan (H_O = 0.4–1.0), and one to nine in invasive Australian (H_O = 0.0–1.0) samples. In addition for 91 Australian samples, only five multilocus genotypes were found (95% of individuals were of two genotypes), suggesting extensive clonality in its introduced range. These loci will be used to examine genetic diversity, hybrid origin and mating system in natural and introduced populations.     

Interactions between a seed‐eating neotropical rodent,the Azara's agouti (Dasyprocta azarae), and the Brazilian ‘pine’ Araucaria angustifolia

We studied the seed predation and scatter‐hoarding behaviour of Azara's agoutis Dasyprocta azarae (Rodentia: Dasyproctidae) in relation to the seeds of the Brazilian ‘pine’, Araucaria angustifolia (Araucariaceae), the rodent's main winter food source. We compared seed‐removal rates, seed‐caching rates, cache distances and recovery rates between a summer period of food abundance (with a low demand for A. angustifolia seeds and no such seeds naturally available) and a winter period of food scarcity (with a high demand for A. angustifolia seeds). We investigated whether the relative seed value affected the rodent's seed‐handling behaviour. We predicted that during the high seed‐demand period (winter): (1) cache distances would be greater; (2) fewer seeds would be stored; (3) more seeds would be recovered and the seed‐recovery time would be lower. In support of our first two predictions, the caching distances were greater in winter (mean ± SE = 15.67 ± 5.11 m) than in summer (9.40 ± 1.59 m), and agoutis hoarded >9 times more seeds in summer (55) than in winter (6). Our third prediction was not supported, and the proportion of unrecovered caches and buried seed recovery times did not differ between winter (mean ± SE = 3.00 ± 0.00 days, n = 5 seeds) and summer (11.05 ± 3.68 days, n = 20 seeds). The high resource density (during summer) rather than the density of A. angustifolia seeds likely influenced seed fate. Agoutis acted mainly as predators, leaving few intact seeds, caching a low proportion of handled seeds (? 8%) and rapidly consuming the caches. Agoutis may cache seeds to keep them safe from competitors on a short‐term basis rather than maintaining medium‐ or long‐term reserves for use during food‐scarcity periods.     

A plea for ‘genealogical thinking’ in comparative biology – a rebuttal to the reply of Szucsich,Wirkner, and Pass to my article ‘Deconstructing Morphology’

Scholtz G. in press. A plea for ‘genealogical thinking’ in comparative biology – a rebuttal to the reply of Szucsich, Wirkner, and Pass to my article ‘Deconstructing Morphology’. —Acta Zoologica (Stockholm) 00 : 1–4. Szucsich et al. (in press) claim that – in contrast to my statement – morphological thinking has to be ‘cladistic.’ Based on this premise, they stress the difference between the relationships among states of characters versus those among structures assigned to the same character state as implemented in numerical cladistic reasoning. SEA claim that my approach to the homology concept only deals with the problem of the integration of various character states into the same character, whereas the necessary relationships among structures assigned to the same state are not covered. Based on this distinction, SEA also criticise the application of similarity in my definition of homology. Furthermore, they address the issue of evolutionarily independent units.     

Multilocus sequence analysis (MLSA) of ‘Rickettsiella costelytrae' and ‘Rickettsiella pyronotae’, intracellular bacterial entomopathogens from New Zealand

Aims

Larvae of scarab beetles live in the soil and are frequently hosts for microbial pathogens. In New Zealand, larvae of the grass grub, Costelytrae zealandica (Coleoptera: Scarabaeidae), and manuka beetles, Pyronota spp. (Coleoptera: Scarabaeidae), have been collected from field populations showing loss of vigour and a whitened appearance. Diagnosis indicated an intracellular infection of fat body tissues by Rickettsiella‐like micro‐organisms. Rickettsiella bacteria are under evaluation as a possible new source of insect bio‐control agents for important agricultural pests as, e.g. scarabaeid and elaterid larvae. The present study aimed at the unequivocal molecular taxonomic identification and comparison of the bacteria associated with Costelytra and Pyronota.

Methods and Results

Electron microscopy and phylogenetic reconstruction using a multilocus sequence analysis approach based on the 16S ribosomal RNA gene together with four protein‐encoding markers (ftsY, gidA, rpsA, and sucB) demonstrated that both bacteria from New Zealand are phylogenetically closely related, but not identical, and belong to the taxonomic genus Rickettsiella.

Conclusions

The bacteria under study should be referred to as pathotypes ‘Rickettsiella costelytrae’ and ‘Rickettsiella pyronotae’, respectively. Moreover, on the basis of the currently accepted systematic organization of the genus Rickettsiella, both pathotypes should be considered synonyms of the nomenclatural type species, Rickettsiella popilliae.

Significance and Impact of the Study

The study demonstrates that Rickettsiella bacteria are geographically widespread pathogens of scarabaeid larvae. Implications of the phylogenetic findings presented for the stability of host adaptation by Rickettsiella bacteria are critically discussed.