Phylogeography and counter-intuitive inferences in island biogeography: evidence from morphometric markers in the mobile butterfly Maniola jurtina (Linnaeus) (Lepidoptera, Nymphalidae)

Distribution of mobile organisms on near-continent islands is mainly shaped by factors operating over ecological rather geological time. However, the phylogeography of single species has the potential to expose historical factors at work. In the present study, West Mediterranean populations of the butterfly Maniola jurtina are studied using geometric morphometrics. The distribution of the two well established lineages ( Maniola jurtina jurtina in the Atlanto–Mediterranean area and Maniola jurtina janira in the Central–Eastern-Mediterranean area) on 12 islands and the adjoining continents are compared. The south-western lineage unexpectedly occurs on islands close to shores occupied by the eastern lineage. We have modelled the distribution of the lineages using three different hypotheses: (1) a contemporary isolation model, which predicts lineage occupancy of islands is linked to relative distances from neighbouring continental areas; (2) a refugial hypothesis, which predicts one lineage to be the ancestral one for the whole region studied, and then successively replaced over part of it; (3) a changing geography hypothesis, which predicts the two lineages to have evolved in their currently occupied areas, continuously sourcing islands subsequent to the Würm maximum glaciation. Of the three models, the refugial hypothesis is most highly correlated with the observed pattern, suggesting that Mediterranean islands may function as refugia during cold periods, much as the three mainland peninsulas of Iberia, Italy and Greece are known to have done. Thereafter, hybridization on the nearest and smallest islands has occurred, with the entire process supporting the notion of the joint influence of factors in ecological and geological time.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 98 , 677–692.     

The role of phytochemistry in dietary choices of Tana River red colobus monkeys(Procolobus badius rufomitratus)

We conducted a phytochemical survey of tree species growing within the riverine forests of the Tana River National Primate Reserve in Kenya to understand better the feeding ecology of an endangered resident primate, the Tana River red colobus monkey (Procolobus badius rufomitratus).Young leaves, which make up a large percentage of this monkey's diet, are significantly higher in nitrogen and lower in acid detergent fiber than more abundant mature leaves are. Phenolic chemistry had little inhibitory effect on feeding by P. b. rufomitratus.Choice among tree species by P. b. rufomitratusappears to be influenced largely by leaf availability,once an acceptable threshold of nitrogen and fiber is reached When mature leaves are eaten, they selected species that are high in nitrogen and low in fiber. A significantly higher nitrogen content was found for the mature leaves of all leguminous versus nonleguminous tree species. Consequently, the availability of certain types of mature leaf species during periods of preferred food scarcity may prove critical to groups of Tana River red colobus monkeys.     

Primate numts and reticulate evolution of capped and golden leaf monkeys (Primates: Colobinae)

A recent phylogenetic study of langurs and leaf monkeys of South Asia suggested a reticulate evolution of capped and golden leaf monkeys through ancient hybridization between Semnopithecus and Trachypithecus. To test this hybridization scenario, I analysed nuclear copies of the mitochondrial cytochrome b gene (numts) from capped, golden and Phayre’s leaf monkeys. These numts were aligned with mitochondrial cytochrome b sequences of various species belonging to the genera Semnopithecus and Trachypithecus. In the phylogenetic tree derived from this alignment, the numts fell into three distinct clades (A, B and C) suggesting three independent integration events. Clade A was basal to Semnopithecus, and clades B and C were basal to Trachypithecus. Among the numts in clades A and C were sequences derived from species not represented in their respective sister mitochondrial groups. This unusual placement of certain numts is taken as additional support for the hybridization scenario. Based on the molecular dating of these integration events, hybridization is estimated to have occurred around 7.1 to 3.4 million years ago. Capped and golden leaf monkeys might have to be assigned to a new genus to reconcile their unique evolutionary history. Additionally, northeast India appears to be a ‘hot spot’ for lineages that might have evolved through reticulate evolution.     

Habitat fragmentation and body‐shape variation of African hind Cephalopholis taeniops (Valenciennes) in an archipelago system (Cape Verde,eastern Atlantic Ocean)

Morphological variations of the serranid fish Cephalopholis taeniops were studied in relation to habitat fragmentation in the Cape Verde Archipelago. While a significant allometric effect existed (11·5% of total body‐shape variation), differences in morphology associated with sex and ontogeny were not significant. MANOVA followed by CVA showed that each island presented a particular allometric pattern. Average body shape for all islands was well discriminated with CVA models. Pair‐wise comparisons of the ontogeny of morphological change between islands revealed that northern islands (Santo Antão, São Vicente and Santa Luzia) along with Boavista Island showed a similar direction in shape ontogeny, while all other paired comparisons indicated different ontogenetic patterns. When comparing directions of inter‐population shape changes, individuals from Fogo Island, the southernmost locality, departed far from the orthogonal relation, suggesting that they were undergoing independent body‐shape trajectories. Physical isolation by geographic distance and depth was positively correlated with morphological divergence among populations from different islands. This finding supports the hypothesis that habitat fragmentation in the Cape Verde Archipelago can be interpreted in terms of marine population structure.     

Genetic differentiation without mimicry shift in a pair of hybridizing Heliconius species (Lepidoptera: Nymphalidae)

Butterflies in the genus Heliconius have undergone rapid adaptive radiation for warning patterns and mimicry, and are excellent models to study the mechanisms underlying diversification. In Heliconius, mimicry rings typically involve distantly related species, whereas closely related species often join different mimicry rings. Genetic and behavioural studies have n how reproductive isolation in many pairs of Heliconius taxa is largely mediated by natural and sexual selection on wing colour patterns. However, recent studies have uncovered new cases in which pairs of closely related species are near‐perfect mimics of each other. Here, we provide morphometric and genetic evidence for the coexistence of two closely related, hybridizing co‐mimetic species on the eastern slopes of the Andes, H. melpomene amaryllis and H. timareta ssp. nov. , which is described here as H. timareta thelxinoe . A joint analysis of multilocus genotyping and geometric morphometrics of wing shape shows a high level of differentiation between the two species, with only limited gene flow and mixing. Some degree of genetic mixing can be detected, but putative hybrids were rare, only one of 175 specimens being a clear hybrid. In contrast, we found phenotypic differentiation between populations of H. timareta thelxinoe , possibly indicative of strong selection for local mimicry in different communities. In this pair of species, the absence of breakdown of genetic isolation despite near‐identical wing patterns implies that factors other than wing patterns keep the two taxa apart, such as chemical or behavioural signals, or ecological adaptation along a strong altitudinal gradient. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109 , 830–847.     

Genetic and morphological variation in a Mediterranean glacial refugium: evidence from Italian pygmy shrews,Sorex minutus (Mammalia: Soricomorpha)

At the Last Glacial Maximum (LGM), the southern European peninsulas were important refugia for temperate species. Current genetic subdivision of species within these peninsulas may reflect past population subdivision at the LGM, as in ‘refugia within refugia’, and/or at other time periods. In the present study, we assess whether pygmy shrew populations from different regions within Italy are genetically and morphologically distinct. One maternally and two paternally inherited molecular markers (cytochrome b and Y‐chromosome introns, respectively) were analysed using several phylogenetic methods. A geometric morphometric analysis was performed on mandibles to evaluate size and shape variability between populations. Mandible shape was also explored with a functional approach that considered the mandible as a first‐order lever affecting bite force. We found genetically and morphologically distinct European, Italian, and southern Italian groups. Mandible size increased with decreasing latitude and southern Italian pygmy shrews exhibited mandibles with the strongest bite force. It is not clear whether or not the southern Italian and Italian groups of pygmy shrews occupied different refugia within the Italian peninsula at the LGM. It is likely, however, that geographic isolation earlier than the LGM on islands at the site of present‐day Calabria was important in generating the distinctive southern Italian group of pygmy shrews, and also the genetic groups in other small vertebrates that we review here. Calabria is an important hotspot for genetic diversity, and is worthy of conservation attention. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 100 , 774–787.     

Adaptive radiation in African weakly electric fish (Teleostei: Mormyridae: Campylomormyrus): a combined molecular and morphological approach

We combined multiple molecular markers and geometric morphometrics to revise the current taxonomy and to build a phylogenetic hypothesis for the African weakly electric fish genus Campylomormyrus. Genetic data (2039 bp DNA sequence of mitochondrial cytochrome b and nuclear S7 genes) on 106 specimens support the existence of at least six species occurring in sympatry. We were able to further confirm these species by microsatellite analysis at 16 unlinked nuclear loci and landmark-based morphometrics. We assigned them to nominal taxa by comparisons to type specimens of all Campylomormyrus species recognized so far. Additionally, we showed that the shape of the elongated trunk-like snout is the major source of morphological differentiation among them. This finding suggests that the radiation of this speciose genus might have been driven by adaptation to different food sources.     

Genetic and morphological differentiation of the mangrove crab Perisesarma guttatum (Brachyura: Sesarmidae) along an East African latitudinal gradient

The genetic structure and morphometric differentiation of mangrove crab Perisesarma guttatum populations were examined among shelf connected locations along a latitudinal gradient on the East African coast. Over 2200 specimens were sampled from 23 mangrove sites for geometric morphometrics analysis. Population genetic analyses of mitochondrial cytochrome c oxidase subunit I (COI) DNA sequences were used to evaluate connectivity among populations. A total of 73 haplotypes were detected, and almost no haplotypes were found in common between two highly supported phylogeographic clades: southern Mozambique (Inhaca Island and Maputo Bay) and a northern clade that included north Mozambique, Tanzania and Kenya. These two clades were identified based on the species' populations pairwise genetic differentiation and geographical location. Φ_ST values were considerably high between the two clades, indicating the presence of significant population genetic structure between Kenya and South Mozambique. However, each clade was composed of genetically similar populations along the latitudinal gradient, and no significant population structure was found within each clade because the Φ_st values were not significant. The morphometric analysis corroborated the division into two clades (i.e. Inhaca Island/Maputo Bay and northern populations) and also detected less shape variation among populations that were few kilometres apart. The significant spatial genetic structuring between the southern and the northern populations of P. guttatum along the geographic gradient under study, combined with morphological differences, suggests that these populations may be considered as cryptic species. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 99 , 28–46.     

The phylogenetic pattern of speciation and wing pattern change in neotropical Ithomia butterflies (Lepidoptera: nymphalidae)

Species level phylogenetic hypotheses can be used to explore patterns of divergence and speciation. In the tropics, speciation is commonly attributed to either vicariance, perhaps within climate-induced forest refugia, or ecological speciation caused by niche adaptation. Mimetic butterflies have been used to identify forest refugia as well as in studies of ecological speciation, so they are ideal for discriminating between these two models. The genus Ithomia contains 24 species of warningly colored mimetic butterflies found in South and Central America, and here we use a phylogenetic hypothesis based on seven genes for 23 species to investigate speciation in this group. The history of wing color pattern evolution in the genus was reconstructed using both parsimony and likelihood. The ancestral pattern for the group was almost certainly a transparent butterfly, and there is strong evidence for convergent evolution due to mimicry. A punctuationist model of pattern evolution was a significantly better fit to the data than a gradualist model, demonstrating that pattern changes above the species level were associated with cladogenesis and supporting a model of ecological speciation driven by mimicry adaptation. However, there was only one case of sister species unambiguously differing in pattern, suggesting that some recent speciation events have occurred without pattern shifts. The pattern of geographic overlap between clades over time shows that closely related species are mostly sympatric or, in one case, parapatric. This is consistent with modes of speciation with ongoing gene flow, although rapid range changes following allopatric speciation could give a similar pattern. Patterns of lineage accumulation through time differed significantly from that expected at random, and show that most of the extant species were present by the beginning of the Pleistocene at the latest. Hence Pleistocene refugia are unlikely to have played a major role in Ithomia diversification.     

The phylogenetic structure of habitat shift and morphological convergence in Asian Clarias (Teleostei, Siluriformes: Clariidae)

Catfishes of the genus Clarias are an important component of the ichthyofauna in Asia and in Africa. Previous studies demonstrated a high diversity in number of species, morphology and habitat, but little was known on the evolutionary processes underlying this diversity. We analysed an original data set of molecular sequences (cytochrome b and 16S genes), habitat and geographic distributions, as well as 29 morphometric measurements taken on 454 specimens of Asian Clarias . Maximum likelihood phylogeny estimation showed an unexpected cryptic diversity due to strong morphological convergence. The patterns of intra- and interspecific phylogenetic divergence are overall explained by geographic isolation. The analysis of habitat transitions with Markovian models showed that Asian Clarias evolved from an ancestor probably living in clear waters. The most frequent transitions occurred between clear and white waters, whereas transitions towards black waters occurred only from clear waters and were rare events. The morphometric analysis suggests a complex pattern of morphological evolution with repeated convergence towards an elongated form in black waters. The phylogeographic patterns of diversification of Asian Clarias agree with previous studies on other groups and the hypothesis that changes in sea level during the Pleistocene had little influence on shaping biodiversity on the Sunda Shelf.     

Categorical versus geometric morphometric approaches to characterizing the evolution of morphological disparity in Osteostraci (Vertebrata,stem Gnathostomata)

Morphological variation (disparity) is almost invariably characterized by two non-mutually exclusive approaches: (1) quantitatively, through geometric morphometrics; and (2) in terms of discrete, ‘cladistic’, or categorical characters. Uncertainty over the comparability of these approaches diminishes the potential to obtain nomothetic insights into the evolution of morphological disparity and the few benchmarking studies conducted so far show contrasting results. Here, we apply both approaches to characterizing morphology in the stem-gnathostome clade Osteostraci in order to assess congruence between these alternative methods as well as to explore the evolutionary patterns of the group in terms of temporal disparity and the influence of phylogenetic relationships and habitat on morphospace occupation. Our results suggest that both approaches yield similar results in morphospace occupation and clustering, but also some differences indicating that these metrics may capture different aspects of morphology. Phylomorphospaces reveal convergence towards a generalized ‘horseshoe’-shaped cranial morphology and two strong trends involving major groups of osteostracans (benneviaspidids and thyestiids), which probably reflect adaptations to different lifestyles. Temporal patterns of disparity obtained from categorical and morphometric approaches appear congruent, however, disparity maxima occur at different times in the evolutionary history of the group. The results of our analyses indicate that categorical and continuous data sets may characterize different patterns of morphological disparity and that discrepancies could reflect preservational limitations of morphometric data and differences in the potential of each data type for characterizing more or less inclusive aspects of overall phenotype.     

Ecogeographical variation in skull morphometry of howler monkeys (Primates: Atelidae)

Our aim is to identify ecomorphological adaptations in the skull shape of the South American howler monkeys (species of the genus Alouatta, Lacépède, 1799, Primates, Atelidae). Since Alouatta is relatively homogenous in feeding ecology, we expect skull shape variation to be relatively conservative across species. We used geometric morphometrics to quantify craniodental morphology in six species of Alouatta. Multivariate regression, two-block Partial Least Squares, and variation partitioning were used to test for the impact of taxonomy, sexual dimorphism, allometry, geography and climate on skull shape. We found morphological overlap among species and sexes, although some discrimination occurs between species living in seasonal environments as opposed to rain forest species. There was a negative latitudinal gradient in skull size across species, with size explaining 34% of total shape variance. Latitude and climate, though important, were secondary in explaining shape variance. Amazonian Alouatta are larger, have thinner molars, wide incisors, and proportionally larger neurocranium. Overall, the shape of southern species seem well adapted to cope with proportionally tougher food items, whereas Amazonian species seem better equipped to deal with a diet richer in fruits, as confirmed by independent field observations. The small size of Alouatta in the South is possibly linked to the effect of competition with the larger folivorous atelid Brachyteles.     

Red kite (Milvus milvus) and black kite (M. migrans): minute genetic interspecies distance of two raptors breeding in a mixed community (Falconiformes: Accipitridae)

Allozyme analysis of 24 loci in 154 red kites (Milvus milvus) and 36 black kites (Milvus migrans) from die Hakel forest (Sachsen-Anhalt, Germany) revealed a Nei's interspecies genetic distance of D = 0.009. Of die observed genetic variance of four polymorphic enzymes, 15.4% referred to die differentiation between die kite species, but 84.6% were contributed by the ingroup polymorphism widiin diese species. Allozymes permit the identification of some 78% of samples as orignating from M. milvus , but only of 5.4% of samples obtained from M. migrans. Akhough the genetic distance is slight, die Milvus kites are valid biospecies which, despite occasional instances of hybridization, coexist sympatrically and may breed in mixed breeding aggregations. Mate choice in die largely separate winter quarters of diese migratory birds or chromosomal incompatibility are hypodietical isolation mechanisms stabilizing die species boundary. Moreover, the range sympatry could have developed fairly recendy widi die spread of human agriculture.     

Morphological evolution in the mandible of spiny rats, genus Trinomys (Rodentia: Echimyidae)

The development and evolution of the rodent mandible have been studied in depth in recent years. The mandible is a complex structure because it consists of six morphogenetic components formed by different condensations of mesenchymal cells. Using recent techniques for the geometric analysis of shape, we have combined developmental information with a powerful quantification of shape variation and an independent estimate of phylogeny (molecular data) to assess the evolutionary patterns of shape change in mandibles of the rodent genus Trinomys . In general, the major trends in shape variation did not agree with the expected phylogenetic pattern. However, for small-scale morphological differences, one species ( T. yonenagae ) was responsible for the lack of association between morphology and molecular divergence. This species is genetically similar to but morphologically different from other Trinomys . The coronoid process was considered to be the most conservative morphogenetic component in the mandible.     

Genomics of the divergence continuum in an African plant biodiversity hotspot,I: drivers of population divergence in Restio capensis (Restionaceae)

Understanding the drivers of population divergence, speciation and species persistence is of great interest to molecular ecology, especially for species‐rich radiations inhabiting the world's biodiversity hotspots. The toolbox of population genomics holds great promise for addressing these key issues, especially if genomic data are analysed within a spatially and ecologically explicit context. We have studied the earliest stages of the divergence continuum in the Restionaceae, a species‐rich and ecologically important plant family of the Cape Floristic Region (CFR) of South Africa, using the widespread CFR endemic Restio capensis (L.) H.P. Linder & C.R. Hardy as an example. We studied diverging populations of this morphotaxon for plastid DNA sequences and >14 400 nuclear DNA polymorphisms from Restriction site Associated DNA (RAD) sequencing and analysed the results jointly with spatial, climatic and phytogeographic data, using a Bayesian generalized linear mixed modelling (GLMM) approach. The results indicate that population divergence across the extreme environmental mosaic of the CFR is mostly driven by isolation by environment (IBE) rather than isolation by distance (IBD) for both neutral and non‐neutral markers, consistent with genome hitchhiking or coupling effects during early stages of divergence. Mixed modelling of plastid DNA and single divergent outlier loci from a Bayesian genome scan confirmed the predominant role of climate and pointed to additional drivers of divergence, such as drift and ecological agents of selection captured by phytogeographic zones. Our study demonstrates the usefulness of population genomics for disentangling the effects of IBD and IBE along the divergence continuum often found in species radiations across heterogeneous ecological landscapes.     

Genetic and morphological differentiation patterns between sister species: the case of Onthophagus taurus and Onthophagus illyricus (Coleoptera, Scarabaeidae)

The present study investigated the morphological and genetic differentiation pattern between two sympatric dung beetle sister species, Onthophagus taurus and Onthophagus illyricus . The geometric morphometric approach coupled with the use of molecular markers allowed examination of the nature of interspecific relationships and an outline of the evolutionary and geographical processes that might have led to interspecific differentiation and the present-day partial sympatric and syntopic pattern of distribution. Geometric morphometrics failed to discrimininate the two species on the ground of external morphological traits, but revealed interspecific differences when the shape of the primary sexual traits was taken into account. The use of two different molecular markers (cytochrome oxidase subunit I gene and amplified fragment-length polymorphism) demonstrates that the two species are genetically well differentiated, forming two distinguishable lineages probably diverged during the Pliocene by allopatric speciation. No evidence of past or recent introgression and no support for hybridization were found, suggesting that sympatry was established subsequently, when speciation was accomplished. Both molecular markers and genital shape indicate that phenotypically intermediate individuals, despite their ambiguous appearance, are members of O. illyricus species rather than hybrids.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 89 , 197–211.