Phylogenomics at the tips: inferring lineages and their demographic history in a tropical lizard,Carlia amax

High‐throughput sequencing approaches offer opportunities to better understand the evolutionary processes driving diversification, particularly in nonmodel organisms. In particular, the 100–1000's of loci that can now be sequenced are providing unprecedented power in population, speciation and phylogenetic studies. Here, we apply an exon capture approach to generate >99% complete sequence and SNP data across >2000 loci from a tropical skink, Carlia amax, and exploit these data to identify divergent lineages and infer their relationships and demographic histories. This is especially relevant to low‐dispersal tropical taxa that often have cryptic diversity and spatially dynamic histories. For C. amax, clustering of nuclear SNPs and coalescent‐based species delimitation analyses identify four divergent lineages, one fewer than predicted based on geographically coherent mtDNA clades (>9.4% sequence divergence). Three of these lineages are widespread and parapatric on the mainland, whereas the most divergent is restricted to islands off the northeast Northern Territory. Tests for population expansion reject an equilibrium isolation‐by‐distance model for two of the three widespread lineages and infer refugial expansion sources in the relatively mesic northeast Top End and northwest Kimberley. The latter is already recognized as a hotspot of endemism, but our results also suggest that a stronger focus on the northeast Top End, and adjacent islands is warranted. More generally, our results show how genome‐reduction methods such as exon capture can yield insights into the pattern and dynamics of biodiversity across complex landscapes with as yet poorly understood biogeographic history and how exon data can link between population and phylogenetic questions.     

Salinity influences the distribution of marine snakes: implications for evolutionary transitions to marine life

Secondary transitions from terrestrial to marine life provide remarkable examples of evolutionary change. Although the maintenance of osmotic balance poses a major challenge to secondarily marine vertebrates, its potential role during evolutionary transitions has not been assessed. In the current study, we investigate the role of oceanic salinity as a proximate physiological challenge for snakes during the phylogenetic transition from the land to the sea. Large‐scale biogeographical analyses using the four extant lineages of marine snakes suggest that salinity constrains their current distribution, especially in groups thought to resemble early transitional forms between the land and the sea. Analyses at the species‐level suggest that a more efficient salt‐secreting gland allows a species to exploit more saline, and hence larger, oceanic areas. Salinity also emerged as the strongest predictor of sea snake richness. Snake species richness was negatively correlated with mean annual salinity, but positively correlated with monthly variation in salinity. We infer that all four independent transitions from terrestrial to marine life in snakes may have occurred in the Indonesian Basin, where salinity is low and seasonally variable. More generally, osmoregulatory challenges may have influenced the evolutionary history and ecological traits of other secondarily marine vertebrates (turtles, birds and mammals) and may affect the impact of climate change on marine vertebrates.     

Navigating the mtDNA road map out of the morphological maze: interpreting morphological variation in the diverse Monomorium rothsteini (Forel) complex (Hymenoptera: Formicidae)

Monomorium is a large and diverse ant genus with speciose radiations in both the Afrotropical and Australian regions. According to the most recent taxonomic revision, many Australian species are characterised by very broad distributions and variable morphology, which suggests that some species may be unrecognised species complexes. With a continent‐wide distribution and diverse yet overlapping morphology, M. rothsteini (Forel) is representative of the greater challenge that exists in Australian Monomorium systematics. Here we investigate species boundaries in M. rothsteini using a molecular phylogenetic framework to interpret the complex overlap of nine morphological characters (with 31 states) and examine biogeographic relationships among the lineages. Bayesian inference resolved 38 mtDNA lineages that were morphologically separable, at least from their sister lineage. Although the morphological characters were intermixed across the phylogeny, instances of inseparable morphology among sister clades was rare. Seventeen lineages exhibited complete morphological overlap with one or more other lineages and could not be separated by Principal Component Analysis based on 12 morphometric variables. Two‐thirds of all lineages occurred sympatrically with one or more both genetically and morphologically divergent lineages. The two nuclear markers EF1αF2 and wingless were used to generate haplotype networks which were characterised by a star‐like pattern indicative of a rapid and recent radiation. Several haplotypes for both nuclear gene regions were shared among individuals occurring in separate mtDNA clades which we were also unable to distinguish morphologically or that were occurring in sympatry, indicating possible introgression in both the mtDNA and nuclear genomes. Clear biogeographic affinities among samples within a lineage were detected but there was no overall pattern in the biogeographic relationships among the lineages. We conclude that M. rothsteini is a large species complex that has undergone a complex evolutionary history following aridification of the Australian continent, and discuss the implications of this conclusion for the systematics of Australian Monomorium more generally.     

Evolutionary lineages of RT1.Ba in the Australian Rattus

In this study, the evolutionary history of the variable second exon of RT1.Ba and its adjoining intron b are compared across a number of species and subspecies of the Australian RATTUS: Three lineages are identified in the second intron across a range of Rattus species. Two of these lineages, separated by the insertion of a probable rodent short interspersed nucleotide element and by point mutations outside the indel region, are both found in each of the major clades of the endemic Australian RATTUS: This pattern of ancestral polymorphism is reflected in the adjoining exon 2 sequences, although phylogenetic constraints confirm that the clustering is not identical to that of the associated intron sequences. In addition, the coding sequences show evidence of the retention of ancestral polymorphism, with identical exon sequences found in two divergent species, and some indication of gene conversion detected for the exon sequences.     

A phylogenetic study of the generic relationships within the subtribe Leucophoropterina Schuh (Miridae: Phylinae: Leucophoropterini)

The subtribe Leucophoropterina (Miridae: Phylinae: Leucophoropterini) is a relatively small lineage of mirids comprising 23 genera and 104 species. Most of the species are endemic to the Indo‐Pacific and Australia, and many are considered ant mimics. A phylogenetic analysis including both the Australian and the Indo‐Pacific taxa was conducted for the first time with a dataset of 137 morphological characters coded for all but two known species of Leucophoropterina. The hypothesis by Schuh ( 1984 ) of at least two major lineages of ant‐mimicking taxa based on his analysis of the Indo‐Pacific taxa continues to be supported with our inclusion of Australian taxa. The Australian taxa and Indo‐Pacific taxa of Leucophoropterina do not form independent, geographically based lineages, but instead comprise several lineages containing taxa from both regions. This study provides a basis for future detailed studies of biogeography and ant mimicry in the group.     

Evolutionary History of the Morocco lizard-Fingered Geckos of the <Emphasis Type="Italic">Saurodactylus brosseti</Emphasis> Complex

Studies of biodiversity in the Maghreb have revealed high genetic diversity and divergent genetic lineages among many taxa including squamates. Geographic barriers such as the Atlas Mountains are one of the key factors promoting genetic differentiation and the high levels of endemism. The lizard-fingered gecko Saurodactylus brosseti is endemic to Morocco. Its range includes both sides of the Atlas Mountains, and although high diversity was previously identified within the species, much of the range was unsampled. To understand the evolutionary and biogeographical history of this species, we used mitochondrial and nuclear DNA sequence data from 64 populations sampled across the entire species range. We employed phylogenetic methods based on gene trees and species trees as well as a time calibrated Bayesian genealogy and coalescent species delimitation approaches. We uncovered four highly divergent and allopatric mitochondrial lineages that did not share haplotypes at variable nuclear loci, suggesting the four groups have been evolving independently since the Miocene, according to our molecular dating estimates. These results coupled with the geographic pattern of genetic diversity suggest a possible role of the Atlas Mountains for the divergence observed between the four lineages of S. brosseti, while each lineage probably later underwent several episodes of fragmentation followed by (re-) expansion during Pleistocene climatic oscillations. Bayesian species delimitation analysis indicates that the four lineages may well be distinct species but we suggest that detailed morphological analyses are needed prior to taxonomic changes. The four lineages represent ancient independent evolutionary units, and deserve conservation management as distinct entities.     

Frequent nonrandom shifts in the temporal sequence of developmental landmark events during teleost evolutionary diversification

Morphological transformations can be generated by evolutionary changes in the sequence of developmental events. In this study, we examined the evolutionary dynamics of the developmental sequence on a macroevolutionary scale in teleosts. Using the information from previous reports describing the development of 31 species, we extracted the developmental sequences of 19 landmark events involving the formation of phylogenetically conserved body parts; we then inferred ancestral developmental sequences by two different parsimony‐based methods—event‐pairing and continuous analysis. The phylogenetic comparisons of these sequences revealed event‐dependent heterogeneity in the frequency of sequence changes. Most of the sequence changes occurred as exchanges of temporally neighboring events. These heterochronic changes in developmental sequences accumulated along evolutionary time, but the precise distribution of the changes over the teleostean phylogeny remains unclear due to technical limitations.     

Seven genes of mitochondrial genome enabling differentiation of honeybee subspecies <Emphasis Type="Italic">Apis mellifera</Emphasis>

On the basis of comparative sequence analysis of 12 honeybee mitochondrial genes, seven genes enabling us to differentiate honeybees subspecies of the A, M, C, O evolutionary lineages were found. Applying comparative sequence analysis of ND2 gene mtDNA as an example on a statistically valid sample size, we showed a high level of differentiating ability of this gene and assumed that each of these seven genes probably can be used for differentiation of the subspecies within four evolutionary lineages.     

Species tree estimation and the historical biogeography of heroine cichlids

Heroine cichlids are major components of the fish faunas in both Central America and the Caribbean. To examine the evolutionary patterns of how cichlids colonized both of these regions, we reconstructed the phylogenetic relationships among 23 cichlid lineages. We used three phylogenetically novel nuclear markers (Dystropin b, Myomesin1, and Wnt7b) in combination with sequence data from seven other gene regions (Nd2, Rag1, Enc1, Sreb2, Ptr, Plagl2, and Zic1) to elucidate the species tree of these cichlids. The species examined represent major heroine lineages in South America, Central America, and the Greater Antilles. The individual gene trees of these groups were topologically quite discordant. Therefore, we combined the genetic partitions and inferred the species tree using both concatenation and a coalescent-based Bayesian method. The two resulting phylogenetic topologies were largely concordant but differed in two fundamental ways. First, more nodes in the concatenated tree were supported with substantial or 100% Bayesian posterior support than in the coalescent-based tree. Second, there was a minor, but biogeographically critical, topological difference between the concatenated and coalescent-based trees. Nevertheless, both analyses recovered topologies consistent with the Greater Antillean heroines being phylogenetically nested within the largely Central American heroine radiation. This study suggests that reconstructions of cichlid phylogeny and historical biogeography should account for the vagaries of individual gene histories.     

Desert spring refugia: museums of diversity or evolutionary cradles?

Refugia play a critical role in preserving species unable to move or adapt to cope with environmental change. The role of refugia as ‘museums of diversity’ means these environments have a high conservation priority. Less well known, however, is the role that isolated and fragmented refugia can play in the generation of new diversity. Here, we examined the diversification and evolutionary history of a community of endemic invertebrates that inhabit Australian desert spring refugia. We compared the phylogenies of seven endemic groups (Haloniscus and Phreatomerus isopods, chiltoniid amphipods, Ngarawa ostracods, Trochidrobia and Fonscochlea snails and Gymnochthebius beetles) from these springs and examine the rates and timing of diversification and reconstructed the phylogeographic history of each taxon. Despite major life‐history differences among these taxa, they demonstrate remarkable similarities in their evolutionary histories. All groups have multiple lineages that extend back to a time before the formation of present‐day deserts, and significant geographic‐based diversification since adapting to a refugial habitat. The results provide further evidence that refugia act as museums of biodiversity, preserving lineages that would have otherwise gone extinct. However, we also observed that isolation in refugia corresponds with significant diversification, leading to a recently evolved, novel endemic fauna, supporting the idea that fragmented refugia provide ideal conditions for the generation of future biodiversity hotspots.     

Sequence diversity of the MHC DRB gene in the Eurasian beaver (Castor fiber)

Major histocompatibility complex (MHC) genes, coding molecules which play an important role in immune response, are the most polymorphic genes known in vertebrates. However, MHC polymorphism in some species is limited. MHC monomorphism at several MHC class I and II loci was previously reported for two neighbouring northern European populations of the Eurasian beaver (Castor fiber) and reduced selection for polymorphism has been hypothesized. Here, we analysed a partial sequence of the second exon of the MHC II DRB locus from seven relict European and Asian beaver populations. We detected 10 unique alleles among 76 beavers analysed. Only a western Siberian population was polymorphic, with four alleles detected in 10 individuals. Each of the remaining populations was fixed for a different allele. Sequences showed considerable divergence, suggesting the long persistence of allelic lineages. A significant excess of nonsynonymous substitutions was detected at the antigen binding sites, indicating that sequence evolution of beaver DRB was driven by positive selection. Current MHC monomorphism in the majority of populations may be the result of the superimposition of the recent bottleneck on pre-existing genetic structure resulting from population subdivision and differential pathogen pressure.     

Molecular survey of morphological subspecies reveals new mitochondrial lineages in Podarcis muralis (Squamata: Lacertidae) from the Tuscan Archipelago (Italy)

Recent analyses of molecular markers have significantly revised the traditional taxonomy of Podarcis species (Squamata: Lacertidae), leading to critically reconsider the taxonomic value of several subspecies described only on morphological bases. In fact, lizards often exhibit high morphological plasticity both at the intra‐specific and the intra‐population level, especially on islands, where phenotypic divergences are mainly due to local adaptation, rather than to evolutionary differentiation. The Common wall lizard Podarcis muralis exhibits high morphological variability in biometry, pholidosis values and colour pattern. Molecular analyses have confirmed the key role played by the Italian Peninsula as a multi‐glacial refuge for P. muralis, pointing out the lack of congruence between mitochondrial lineages and the four peninsular subspecies currently recognized. Here, we analyse a portion of the protein‐encoding cytochrome b gene in the seven subspecies described for the Tuscan Archipelago (Italy), in order to test whether the mitochondrial haplotypes match the morphologically based taxonomy proposed for Common wall lizard. We also compare our haplotypes with all the others from the Italian Peninsula to investigate the presence of unique genetic lineages in insular populations. Our results do not agree completely with the subspecific division based on morphology. In particular, the phylogenetic analyses show that at least four subspecies are characterized by very similar haplotypes and fall into the same monophyletic clade, whereas the other three subspecies are closer to peninsular populations from central Italy. From these results, we conclude that at least some subspecies could be better regarded as simple eco‐phenotypes; in addition, we provide an explanation for the distinctiveness of exclusive lineages found in the archipelago, which constituted a refuge for this species during last glacial periods.     

Competition and facilitation between Australian and Spanish legumes in seven Australian soils

This paper evaluates the relative performance and competitive ability of seven legumes from the Iberian Peninsula, Spain (one already invasive in Australia), grown singly or pairwise with seven legumes from south‐western Australia in their own soils. Indices of growth used were root, shoot and total mass and shoot dimensions. Water content, xylem water potential during drying and nodule production were also measured. The index of competition used was the intensity of competition coefficient (ICC), which is suitable for additive designs. The Australian species usually grew larger than the Spanish species, in their presence or absence, although the results were sensitive to the index of growth or resource capture used. The Australian legumes usually possessed greater total water content than the co‐occurring Spanish legumes. At least five Australian species were less reduced or not affected at all by inter‐regional competition compared with growth in isolation. Two Australian legumes performed relatively poorly in the presence of at least four Spanish legumes. The ICC identified many instances of growth promotion (facilitation) of the Australian species, which we attribute to extra nitrogen obtained through enhanced nodulation of both cohabiting species. Five of the seven Spanish species were outcompeted by the Australian species, whereas the growth of two was sometimes facilitated. Although the Spanish legumes had greater competitive ability in the more fertile Australian soils, they remained competitively inferior to the Australian legumes in their first season of growth and none is likely to displace the native legumes at this stage of growth. Longer‐term field studies are needed to fully evaluate the potential invasiveness of perennial legumes.     

The evolution of sexual and parthenogenetic Warramaba: a window onto Plio–Pleistocene diversification processes in an arid biome

Environmental changes over the Plio‐Pleistocene have been key drivers of speciation patterns and genetic diversification in high‐latitude and mesic environments, yet comparatively little is known about the evolutionary history of species in arid environments. We applied phylogenetic and phylogeographic analyses to understand the evolutionary history of Warramaba grasshoppers from the Australian arid zone, a group including sexual and parthenogenetic lineages. Sequence data (mitochondrial COI) showed that the four major sexual lineages within Warramaba most likely diverged in the Pliocene, around 2–7 million years ago. All sexual lineages exhibited considerable phylogenetic structure. Detailed analyses of the hybrid parthenogenetic species W. virgo and its sexual progenitors showed a pattern of high phylogenetic diversity and phylogeographic structure in northern lineages, and low diversity and evidence for recent expansion in southern lineages. Northern sexual lineages persisted in localized refugia over the Pleistocene, with sustained barriers promoting divergence over this period. Southern parts of the present range became periodically unsuitable during the Pleistocene, and it is into this region that parthenogenetic lineages have expanded. Our results strongly parallel those for sexual and parthenogenetic lineages of the gecko Heteronotia from the same region, indicating a highly general effect of Plio‐Pleistocene environmental change on diversification processes in arid Australia.