The phylogeny and biogeography of Hakea (Proteaceae) reveals the role of biome shifts in a continental plant radiation

The frequency of evolutionary biome shifts during diversification has important implications for our ability to explain geographic patterns of plant diversity. Recent studies present several examples of biome shifts, but whether frequencies of biome shifts closely reflect geographic proximity or environmental similarity of biomes remains poorly known. We explore this question by using phylogenomic methods to estimate the phylogeny of Hakea, a diverse Australian genus occupying a wide range of biomes. Model‐based estimation of ancestral regions indicates that Hakea began diversifying in the Mediterranean biome of southern Australia in the Middle Eocene–Early Oligocene, and dispersed repeatedly into other biomes across the continent. We infer around 47 shifts between biomes. Frequencies of shifts between pairs of biomes are usually similar to those expected from their geographic connectedness or climatic similarity, but in some cases are substantially higher or lower than expected, perhaps reflecting how readily key physiological traits can be modified to adapt lineages to new environments. The history of frequent biome‐shifting is reflected in the structure of present‐day assemblages, which tend to be more phylogenetically diverse than null‐model expectations. The case of Hakea demonstrates that the radiation of large plant clades across wide geographic areas need not be constrained by dispersal limitation or conserved adaptations to particular environments.     

Repeated evolution of terrestrial lineages in a continental lizard radiation

The “early‐burst” model of adaptive radiation predicts an early increase in phenotypic disparity concurrent with lineage diversification. Although most studies report a lack of this coupled pattern, the underlying processes are not identified. The continental radiation of Hemidactylus geckos from Peninsular India includes morphologically diverse species that occupy various microhabitats. This radiation began diversifying ~36 Mya with an early increase in lineage diversification. Here, we test the “early‐burst” hypothesis by investigating the presence of ecomorphs and examining the pattern of morphological diversification in a phylogenetic framework. Two ecomorphs—terrestrial and scansorial species—that vary significantly in body size and toepad size were identified. Unlike the prediction of the “early‐burst” model, we find that disparity in toepad morphology accumulated more recently ~14 Mya and fit the Ornstein‐Ulhenbeck model. Ancestral state reconstruction of the two ecomorphs demonstrates that terrestrial lineages evolved independently at least five times from scansorial ancestors, with the earliest diversification in terrestrial lineages 19–12 Mya. Our study demonstrates a delayed increase in morphological disparity as a result of the evolution of terrestrial ecomorphs. The diversification of terrestrial lineages is concurrent with the establishment of open habitat and grasslands in Peninsular India, suggesting that the appearance of this novel resource led to the adaptive diversification.     

Diversification across a heterogeneous landscape

Adaptation to contrasting environments across a heterogeneous landscape favors the formation of ecotypes by promoting ecological divergence. Patterns of fitness variation in the field can show whether natural selection drives local adaptation and ecotype formation. However, to demonstrate a link between ecological divergence and speciation, local adaptation must have consequences for reproductive isolation. Using contrasting ecotypes of an Australian wildflower, Senecio lautus in common garden experiments, hybridization experiments, and reciprocal transplants, we assessed how the environment shapes patterns of adaptation and the consequences of adaptive divergence for reproductive isolation. Local adaptation was strong between ecotypes, but weaker between populations of the same ecotype. F1 hybrids exhibited heterosis, but crosses involving one native parent performed better than those with two foreign parents. In a common garden experiment, F2 hybrids exhibited reduced fitness compared to parentals and F1 hybrids, suggesting that few genetic incompatibilities have accumulated between populations adapted to contrasting environments. Our results show how ecological differences across the landscape have created complex patterns of local adaptation and reproductive isolation, suggesting that divergent natural selection has played a fundamental role in the early stages of species diversification.     

Diversification in the Mexican horned lizard Phrynosoma orbiculare across a dynamic landscape

The widespread montane Mexican horned lizard Phrynosoma orbiculare (Squamata: Phrynosomatidae) represents an ideal species to investigate the relative impacts of Neogene vicariance and Quaternary climate change on lineage diversification across the Mexican highlands. We used mitochondrial DNA to examine the maternal history of P. orbiculare and estimate the timing and tempo of lineage diversification. Based on our results, we inferred 11 geographically structured, well supported mitochondrial lineages within this species, suggesting P. orbiculare represents a species complex. Six divergences between lineages likely occurred during the Late Miocene and Pliocene, and four splits probably happened during the Pleistocene. Diversification rate appeared relatively constant through time. Spatial and temporal divergences between lineages of P. orbiculare and co-distributed taxa suggest that a distinct period of uplifting of the Transvolcanic Belt around 7.5-3 million years ago broadly impacted diversification in taxa associated with this mountain range. To the north, several river drainages acting as filter barriers differentially subdivided co-distributed highland taxa through time. Diversification patterns observed in P. orbiculare provide additional insight into the mechanisms that impacted differentiation of highland taxa across the complex Mexican highlands.     

Uncovering Cryptic Diversity in Two Amoebozoan Species Using Complete Mitochondrial Genome Sequences

The Amoebozoa are a major eukaryotic lineage that encompasses a wide range of amoeboid organisms. The group is understudied from a systematic perspective: molecular tools have only been applied in the last 15 yr. Hence, there is an undersampling of both genes and taxa in the group especially compared to plants, animals, and fungi. Here, we present the complete mitochondrial genomes of two ubiquitous and abundant morpho‐species (Acanthamoeba castellanii and Vermamoeba vermiformis). Both have mitochondrial genomes of close relatives previously available, enabling insights into recent divergences at a genomic scale, while simultaneously offering comparisons with divergence estimates obtained from traditionally used single genes, SSU rDNA and cox1. The newly sequenced mt genomes are significantly divergent from their previously sequenced conspecifics (A. castellannii 16.4% divergence at nucleotide level and 10.4% amino acid; V. vermiformis 21.6% and 13.1%, respectively), while divergence at the small subunit ribosomal DNA is below 1% within both species. Morphological analyses determined that these lineages are indistinguishable from their previously sequenced counterparts. Phylogenetic reconstructions using 26 mt genes also indicate a level of divergence that is comparable to divergence among species, while reconstructions using the small subunit ribosomal DNA (SSU rDNA) do not. In addition, we demonstrate that between closely related taxa, there are high levels of synteny, which can be explored for primer design to obtain larger fragments than the traditional barcoding genes. We conclude that, although most systematic work has relied on SSU, this gene alone can severely underestimate diversity. Thus, we suggest that the mt genome emerges as an alternative for unraveling the lower level phylogenetic relationships of Amoebozoa.     

Herpetofaunal species presence in buffel grass (Cenchrus ciliaris) versus native vegetation‐dominated habitats at Uluṟu‐Kata Tjuṯa National Park

Buffel grass (Cenchrus ciliaris) has been established in Ulu?u‐Kata Tjut a National Park since 1968. To date, the influence of buffel grass on the Park's flora and fauna has been largely unassessed. The objectives of this study were to determine if buffel grass dominates vegetation communities at the base of Ulu?u and if buffel grass habitats are associated with lower reptile and amphibian species richness than endemic vegetation communities. We used vegetation transects to measure the amount of buffel grass and genera of endemic vegetation at 26 sampling locations around the base of Ulu?u. The vegetation survey data were paired with pitfall trap data from reptile and amphibian captures at the same sampling locations. Indicator species analysis and non‐metric multidimensional scaling were used to analyse the vegetation and herpetofaunal community data. Our analyses determined five distinct vegetation communities around Ulu?u. At the base of Ulu?u, buffel grass dominated half of sampled areas and the rest of the inselberg's base was dominated by Themeda grasses. Buffel grass habitats had significantly higher herpetofaunal species richness than the Themeda habitats that dominated other areas at Ulu?u's base. Herpetofauna species richness in buffel grass‐dominated habitats was also significantly higher than all vegetation communities except for Triodia‐dominated habitats. These observations do not directly indicate that buffel grass presence promotes higher species richness of reptiles and amphibians since the observed patterns may be driven by factors such as proximity to breeding sites and abiotic variables not directly related to the grass itself.     

High dispersal ability inhibits speciation in a continental radiation of passerine birds

Dispersal can stimulate speciation by facilitating geographical expansion across barriers or inhibit speciation by maintaining gene flow among populations. Therefore, the relationship between dispersal ability and speciation rates can be positive or negative. Furthermore, an 'intermediate dispersal' model that combines positive and negative effects predicts a unimodal relationship between dispersal and diversification. Because both dispersal ability and speciation rates are difficult to quantify, empirical evidence for the relationship between dispersal and diversification remains scarce. Using a surrogate for flight performance and a species-level DNA-based phylogeny of a large South American bird radiation (the Furnariidae), we found that lineages with higher dispersal ability experienced lower speciation rates. We propose that the degree of fragmentation or permeability of the geographical setting together with the intermediate dispersal model are crucial in reconciling previous, often contradictory findings regarding the relationship between dispersal and diversification.     

Divergent character clines across a recent secondary contact zone in a Hispaniolan lizard

Studies of genetic contact zones provide valuable information regarding the processes of population divergence, adaptation and speciation. In this paper, I examine transitions in morphology, mitochondrial DNA (mtDNA) and nuclear DNA (nDNA) haplotypes across a recent secondary contact zone in a Hispaniolan lizard Ameiva chrysolaema . Maximum likelihood cline fitting analyses suggest non-coincidence of cline centers and that the mtDNA cline is significantly displaced to the west of the remaining clines. nDNA and morphological clines are coincident and tend to be associated with the prevailing environmental gradient. The lack of cytonuclear disequilibrium near the center of the contact zone and the non-coincidence of character clines suggest that this zone does not conform to a tension zone model of hybridization; thus, gene flow across the zone does not seem to be impeded. The extremely narrow width of the dorsal scale size cline and the close association of this cline with the steepness of the environmental (precipitation) gradient suggest that this character may be under environmental selection. Taken together, this contact zone appears to be structured by a combination of mtDNA introgression, possibly associated with eastward movement of the zone, and environmental selection on some characters.     

Waves of parthenogenesis in the desert: evidence for the parallel loss of sex in a grasshopper and a gecko from Australia

The rarity of parthenogenesis, reproduction without sex, is a major evolutionary puzzle. To understand why sexual genetic systems are so successful in nature, we must understand why parthenogenesis sometimes evolves and persists. Here we use DNA sequence data to test for similarities in the tempo and mode of the evolution of parthenogenesis in a grasshopper and a lizard from the Australian desert. We find spectacular congruence between genetic and geographic patterns of parthenogenesis in these distantly related organisms. In each species, parthenogenesis evolved twice and appears to have expanded in parallel waves across the desert, suggesting a highly general selective force against sex.     

Host‐associated genetic differentiation in a seed parasitic weevil Rhinusa antirrhini (Coleptera: Curculionidae) revealed by mitochondrial and nuclear sequence data

Plant feeding insects and the plants they feed upon represent an ecological association that is thought to be a key factor for the diversification of many plant feeding insects, through differential adaptation to different plant selective pressures. While a number of studies have investigated diversification of plant feeding insects above the species level, relatively less attention has been given to patterns of diversification within species, particularly those that also require plants for oviposition and subsequent larval development. In the case of plant feeding insects that also require plant tissues for the completion of their reproductive cycle through larval development, the divergent selective pressure not only acts on adults, but on the full life history of the insect. Here we focus attention on Rhinusa antirrhini (Curculionidae), a species of weevil broadly distributed across Europe that both feeds on, and oviposits and develops within, species of the plant genus Linaria (Plantaginaceae). Using a combination of mtDNA (COII) and nuclear DNA (EF1‐α) sequencing and copulation experiments we assess evidence for host associated genetic differentiation within R. antirrhini. We find substantial genetic variation within this species that is best explained by ecological specialisation on different host plant taxa. This genetic differentiation is most pronounced in the mtDNA marker, with patterns of genetic variation at the nuclear marker suggesting incomplete lineage sorting and/or gene flow between different host plant forms of R. antirrhini, whose origin is estimated to date to the mid‐Pliocene (3.77 Mya; 2.91–4.80 Mya).     

Long forsaken species diversity in the Middle American lizard Holcosus undulatus (Teiidae)

Numerous reptile species have been divided into subspecies. Although this classification may capture the morphological variation within species, it often conceals significant species diversity because many subspecies actually represent species under lineage‐based species concepts. The lizard Holcosus undulatus is a common, widely distributed, monotypic species in Middle America. However, 12 subspecies of this taxon were recognized until the early 1970s. We used two lineage‐based methods for species delimitation to re‐evaluate species limits within H. undulatus with DNA sequence and morphological data. We included all the previously recognized subspecies of H. undulatus except H. u. miadis. Holcosus undulatus was exclusive. In addition, H. u. amphigrammus, H. u. gaigeae, H. u. hartwegi, H. u. parvus, H. u. pulcher, H. u. sinister, H. u. stuarti, H. u. thomasi and H. u. undulatus were supported as distinct evolutionary lineages based on the molecular and morphological evidence. We therefore elevate all of these subspecies to species rank. In addition, two separate mitochondrial lineages may represent cryptic, undescribed species within H. undulatus. The morphological distinctness and allopatry of H. u. miadis and H. u. pulcher, as well as the high genetic divergence of the latter species, suggest that they also represent distinct evolutionary species. Our results also suggest that additional species diversity may still be hidden within the H. u. amphigrammus, H. u. parvus, H. u. sinister and H. u. undulatus lineages. This work supports resurrection of overlooked diversity within Holcosus, which has important implications for the conservation of this genus in Middle America. © 2015 The Linnean Society of London     

Evolutionary divergence in freshwater insects with contrasting dispersal capacity across a sea of desert

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Ficus racemosa is pollinated by a single population of a single agaonid wasp species in continental South‐East Asia

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