A tale of North and South America: time and mode of dispersal of the amphitropical genus Munroa (Poaceae,Chloridoideae)

Plant disjunctions have provided some of the most intriguing distribution patterns historically addressed by biogeographers. We evaluated the three hypotheses that have been postulated to explain these patterns [vicariance, stepping‐stone dispersal and long‐distance dispersal (LDD)] using Munroa, an American genus of grasses with six species and a disjunct distribution between the desert regions of North and South America. The ages of clades, cytology, ancestral characters and areas of distribution were investigated in order to establish relationships among species, to determine the time of divergence of the genus and its main lineages, and to understand further the biogeographical and evolutionary history of this genus. Bayesian inference recovered the North American M. pulchella as sister species to the rest. Molecular dating and ancestral area analyses suggest that Munroa originated in North America in the late Miocene–Pliocene (7.2 Mya; 8.2–6.5 Mya). Based on these results, we postulate that two dispersal events modelled the current distribution patterns of Munroa: the first from North to South America (7.2 Mya; 8.2–6.5 Mya) and the second (1.8 Mya; 2–0.8 Mya) from South to North America. Arid conditions of the late Miocene–Pliocene in the Neogene and Quaternary climatic oscillations in North America and South America were probably advantageous for the establishment of populations of Munroa. We did not find any relationship between ploidy and dispersal events, and our ancestral character analyses suggest that shifts associated with dispersal and seedling establishment, such as habit, reproductive system, disarticulation of rachilla, and shape and texture of the glume, have been important in these species reaching new areas. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 179 , 110–125.     

Extending ecological niche models to the past 120 000 years corroborates the lack of strong phylogeographic structure in the Crested Drongo (Dicrurus forficatus forficatus) on Madagascar

We conduct a phylogeographic study of the Crested Drongo (Dicrurus forficatus forficatus), a broadly distributed bird species on Madagascar. We first determined the demographic and spatial pattern inferred from mitochondrial and nuclear data, and then compared these results with predictions from a present to 0.120‐Myr‐old reconstruction of the spatial dynamics of the range of D. f. forficatus on Madagascar, enabling putative areas of stability (lineage persistence) to be detected. Weak genetic structure along an east–west pattern and comparatively low genetic diversity were recovered, with strong evidence of population expansion found at all ten loci sampled. The palaeoclimatic distribution models over the past 0.120 Myr suggest the presence of extensive areas of suitable climate in the east and west for the species since its colonization of Madagascar, a result in strong concordance with the spatial and genetic signal derived from our multilocus data set. © 2013 The Linnean Society of London     

Phylogeographic diversification of antelope squirrels (Ammospermophilus) across North American deserts

We investigated the biogeographic history of antelope squirrels, genus Ammospermophilus, which are widely distributed across the deserts and other arid lands of western North America. We combined range‐wide sampling of all currently recognized species of Ammospermophilus with a multilocus data set to infer phylogenetic relationships. We then estimated divergence times within identified clades of Ammospermophilus using fossil‐calibrated and rate‐calibrated molecular clocks. Lastly, we explored generalized distributional changes of Ammospermophilus since the last glacial maximum using species distribution models, and assessed responses to Quaternary climate change by generating demographic parameter estimates for the three wide‐ranging clades of A. leucurus. From our phylogenetic estimates we inferred strong phylogeographic structure within Ammospermophilus and the presence of three well‐supported major clades. Initial patterns of historical divergence were coincident with dynamic alterations in the landscape of western North America, and the formation of regional deserts during the Late Miocene and Pliocene. Species distribution models and demographic parameter estimates revealed patterns of recent population expansion in response to glacial retreat. When combined with evidence from co‐distributed taxa, the historical biogeography of Ammospermophilus provides additional insight into the mechanisms that impacted diversification of arid‐adapted taxa across the arid lands of western North America. We propose species recognition of populations of the southern Baja California peninsula to best represent our current understanding of evolutionary relationships among genetic units of Ammospermophilus. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109 , 949–967.     

Distribution,host plant affiliation,phenology, and phylogeny of walnut‐infesting Rhagoletis flies (Diptera: Tephritidae) in Mexico

Many taxa of Nearctic origin have diversified in the subtropical highlands of Mexico. In particular, flies in the genus Rhagoletis have undergone episodes of isolation and gene flow during Pleistocene glaciations and post‐glacial times that have produced lineage differentiation and reproductive isolation. To reach a better understanding of the phylogeography of the genus Rhagoletis, a host plant survey of the walnut‐infesting Rhagoletis suavis species group was conducted across sixteen states comprising 34 different collecting sites in Mexico over a 9‐year period. Five species of Juglans were found to be infested by three species of walnut‐attacking Rhagoletis flies. Several species of parasitoids were also recovered from collections, but in contrast to their walnut fly hosts, they revealed little evidence for host or geographic subdivision. There was no consistent difference in mean eclosion time between walnut fly species or populations associated with different host walnuts in Mexico, unlike the case for other Rhagoletis species, in which allochronic isolation arising from variation in diapause timing is a major ecological adaptation, reproductively isolating flies. We compare the distribution of R. suavis flies in Mexico with those of other Rhagoletis species attacking hawthorns and cherries, and discuss its implications for population divergence and speciation. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 110 , 765–779.     

New insights into the phylogenetics and biogeography of Arum (Araceae): unravelling its evolutionary history

The heat‐ and odour‐producing genus Arum (Araceae) has interested scientists for centuries. This long‐term interest has allowed a deep knowledge of some complex processes, such as the physiology and dynamics of its characteristic lure‐and‐trap pollination system, to be built up. However, mainly because of its large distributional range and high degree of morphological variation, species' limits and relationships are still under discussion. Today, the genus comprises 28 species subdivided into two subgenera, two sections and six subsections. In this study, the phylogeny of the genus is inferred on the basis of four plastid regions, and the evolution of several morphological characters is investigated. Our phylogenetic hypothesis is not in agreement with the current infrageneric classification of the genus and challenges the monophyly of several species. This demonstrates the need for a new infrageneric classification based on characters reflecting the evolution of this enigmatic genus. To investigate the biogeography of Arum deeply, further spatiotemporal analyses were performed, addressing the importance of the Mediterranean basin in the diversification of Arum. Our results suggest that its centre of origin was the European–Aegean region, and that major diversification happened during the last 10 Myr. © 2010 The Linnean Society of London, Botanical Journal of the Linnean Society, 2010, 163 , 14–32.     

Phylogenetics of Escallonia (Escalloniaceae) based on plastid DNA sequence data

Escallonia (Escalloniaceae) is a New World genus of c. 39 species distributed mainly in the South American highlands. Plastid DNA sequence data from the intergenic spacers trnS‐trnG and 3′ trnV‐ndhC and the ndhF gene for 32 species were used to examine the relationships among species and related genera and to analyse the relationship between phylogeny and the geographical distribution of the species. Maximum parsimony and Bayesian inference were employed to analyse the data. The sister relationship of Escallonia to Forgesia and Valdivia was corroborated. We recovered five strongly supported clades that are geographically structured, suggesting that the evolutionary history of the genus may be linked to historical processes, including the uplift of mountainous systems in South America. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 173 , 442–451.     

A new genus of Entiminae from North Africa,supported by a phylogenetic analysis (Coleoptera: Curculionidae: Entiminae)

The genus Holcophloeus gen. nov. is here proposed to include Trachyphloeus cruciatus Seidlitz, 1868, and two new species native to North Africa, based on a phylogenetic analysis and an evaluation of the diagnostic characters. The taxonomic position of Holcophloeus in relation to the tribes Trachyphloeini Lacordaire, 1863, and Holcorhinini Desbrochers, 1898, is discussed, and the new genus is attributed to the Holcorhinini. Holcophloeus laurae sp. nov. from south‐eastern Morocco and Holcophloeus weilli sp. nov. from northern Libya are described and illustrated and a key to the species of the new genus is given. The lectotype of Trachyphloeus cruciatus Seidlitz, 1868, is designated. The genus Massimiellus Borovec, 2009, is transferred from Trachyphloeini to Holcorhinini. © 2013 The Linnean Society of London     

Phylogenetic and biogeographical relationships of the Sander pikeperches (Percidae: Perciformes): patterns across North America and Eurasia

North America and Eurasia share several closely related taxa that diverged either from the breakup of the Laurasian supercontinent or later closures of land bridges. Their modern population structures were shaped in Pleistocene glacial refugia and via later expansion patterns, which are continuing. The pikeperch genus Sander contains five species – two in North America (S. canadensis and S. vitreus) and three in Eurasia (S. lucioperca, S. marinus, and S. volgensis) – whose evolutionary relationships and relative genetic diversities were previously unresolved, despite their fishery importance. This is the first analysis to include the enigmatic and rare sea pikeperch S. marinus, nuclear DNA sequences, and multiple mitochondrial DNA regions. Bayesian and maximum‐likelihood trees from three mitochondrial and three nuclear gene regions support the hypothesis that Sander diverged from its sister group Romanichthys/Zingel ～24.6 Mya. North American and Eurasian Sander then differentiated ～20.8 Mya, with the former diverging ～15.4 Mya, congruent with North American fossils dating to ～16.3–13.6 Mya. Modern Eurasian species date to ～13.8 Mya, with S. volgensis being basal and comprising the sister group to S. lucioperca and S. marinus, which diverged ～9.1 Mya. Genetic diversities of the North American species are higher than those in Eurasia, suggesting fewer Pleistocene glaciation bottlenecks. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 110 , 156–179.     

Effects of changing climate on species diversification in tropical forest butterflies of the genus Cymothoe (Lepidoptera: Nymphalidae)

Extant clades may differ greatly in their species richness, suggesting differential rates of species diversification. Based on phylogenetic trees, it is possible to identify potential correlates of such differences. Here, we examine species diversification in a clade of 82 tropical African forest butterfly species (Cymothoe), together with its monotypic sister genus Harma. Our aim was to test whether the diversification of the Harma–Cymothoe clade correlates with end‐Miocene global cooling and desiccation, or with Pleistocene habitat range oscillations, both postulated to have led to habitat fragmentation. We first generated a species‐level phylogenetic tree for Harma and Cymothoe, calibrated within an absolute time scale, and then identified temporal and phylogenetic shifts in species diversification. Finally, we assessed correlations between species diversification and reconstructed global temperatures. Results show that, after the divergence of Harma and Cymothoe in the Miocene (15 Mya), net species diversification was low during the first 7 Myr. Coinciding with the onset of diversification of Cymothoe around 7.5 Mya, there was a sharp and significant increase in diversification rate, suggesting a rapid radiation, and correlating with a reconstructed period of global cooling and desiccation in the late Miocene, rather than with Pleistocene oscillations. Our estimated age of 4 Myr for a clade of montane species corresponds well with the uplift of the Eastern Arc Mountains where they occur. We conclude that forest fragmentation caused by changing climate in the late Miocene as well as the Eastern Arc Mountain uplift are both likely to have promoted species diversification in the Harma–Cymothoe clade. Cymothoe colonized Madagascar much later than most other insect lineages and, consequently, had less time available for diversification on the island. We consider the diversification of Cymothoe to be a special case compared with other butterfly clades studied so far, both in terms of its abrupt diversification rate increase and its recent occurrence (7 Myr). It is clear that larval host plant shift(s) cannot explain the difference in diversification between Cymothoe and Harma; however, such a shift(s) may have triggered differential diversification rates within Cymothoe. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, ●● , ●●–●●.     

Morphological adaptation to coastal marshes in spite of limited genetic structure in the Neotropical passerine Spartonoica maluroides (Aves: Furnariidae)

Tidal marshes present profound adaptive challenges to terrestrial vertebrates. For example, North American sparrows have relatively longer and thinner bills and darker dorsal plumage in coastal saltmarshes than in interior marshes. Bay‐capped wren‐spinetail (Furnariidae; Spartonoica maluroides) show a strong association with South American saltmarshes. We hypothesized that bay‐capped wren‐spinetail have similar morphological adaptations to North American sparrows to the saltmarsh environment, which would be indicative of the generality of selection on these traits in the coastal saltmarsh ecosystem. We captured individuals of S. maluroides from coastal saltmarshes and interior marshes. Populations were compared based on morphology and molecular markers. We found significant phenotypic differences in bill shape and plumage coloration (melanism) between S. maluroides populations from coastal and inland marshes. The low levels of genetic variation, weak geographical structure and shallow divergences, based on mitochondrial DNA and microsatellite data, suggest that coastal populations had a recent demographic expansion. Our results are consistent with the pattern of morphological divergence found between North American Emberizids. The possibility of convergent evolutionary adaptations between saltmarsh North American Emberizids and South American Furnariids suggests that there are strong selective pressures associated with saltmarsh environments on the beak, leading to adaptations for food acquisition, and on plumage coloration for better camouflage for predator avoidance (melanism). © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109 , 78–91.     

Application of plastid and nuclear markers to DNA barcoding of Euro‐Mediterranean oaks (Quercus,Fagaceae): problems,prospects and phylogenetic implications

DNA barcoding, a species identification system based on sequences from a short, standardized DNA region, has emerged recently as a new tool for taxonomists. We investigated the discriminatory power of a subset of highly variable proposed plant barcoding loci (matK, trnH‐psbA, ITS2) in Quercus, a taxonomically complex tree genus of global importance. The research included all currently recognized species and some major variants of the Mediterranean region and Europe (32 taxa) and 17 East Asian and North American species used for comparison. Based on sequence character state, we assigned unique plastid haplotypes to 40.8% of the investigated species; ITS2 increased the resolution up to 87.8% of total taxa. Nevertheless, unsuccessful genetic distance‐based discrimination questioned the potential efficiency of correct species identification for future studies. Most species appeared to be nonmonophyletic in parallel phylogenetic tests. Three subgeneric groups were outlined, with different rates of within‐group variability and geographical differentiation. Members of one of these groups (corresponding to the Eurasian Group Ilex) were paraphyletic to Group Quercus from the New and Old World and the Eurasian Group Cerris. The data gathered indicate that barcoding markers may help to identify closely related species clusters and contribute to the inference of major diversification and evolutionary patterns in oaks, but the methodology per se appears to be of limited efficacy in defining species limits, unless we make a profound revision of traditional Quercus taxonomic categories. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 172 , 478–499.     

Phylogenetic revision of the Hippasterinae (Goniasteridae; Asteroidea): systematics of deep sea corallivores,including one new genus and three new species

The Hippasterinae is a subfamily within the Goniasteridae, consisting of five genera and 26 species, which occur in cold‐water settings ranging from subtidal to abyssal depths. All known genera were included in a cladistic analysis resulting in two most parsimonious trees, supporting the Hippasterinae as monophyletic. Our review supports Sthenaster emmae gen. et sp. nov. as a new genus and species from the tropical Atlantic and two new Evoplosoma species, Evoplosoma claguei sp. nov. and Evoplosoma voratus sp. nov. from seamounts in the North Pacific. Hippasteria caribaea is reassigned to the genus Gilbertaster, which previously contained a single Pacific species. Our analysis supports Evoplosoma as a derived deep water lineage relative to its continental‐shelf, shallow water sister taxa. The genus Hippasteria contains approximately 15 widely distributed, but similar‐looking species, which occur in the northern and southern hemispheres. Except for Gilbertaster, at least one species in each genus has been observed or is inferred to prey on deep‐sea corals, suggesting that this lineage is important to the conservation of deep‐sea coral habitats. The Hippasterinae shares several morphological similarities with Circeaster and Calliaster, suggesting that they may be related. © 2010 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 160 , 266–301.     

Taxonomic revision of the genus Galictis (Carnivora: Mustelidae): species delimitation,morphological diagnosis,and refined mapping of geographical distribution

Although critical for enabling in‐depth evolutionary, ecological, or conservation‐orientated studies, taxonomic knowledge is still scarce for many groups of organisms, including mammals of the order Carnivora. For some of these taxa, even basic aspects such as species limits and geographical distribution are still uncertain. This is the case for the Neotropical mustelid genus Galictis, considered one of the least studied carnivoran genera in the Americas. To address this issue, we performed a comprehensive assessment of morphological and molecular characters to test the number of species within Galictis, and to characterize their distinctiveness and evolutionary history. In addition, we reviewed and consolidated the available information on the taxonomy of this genus, so as to provide a historical framework upon which we could interpret our data. Our analyses demonstrated that two Galictis species can be clearly delimited and diagnosed using metric and nonmetric morphological characters as well as DNA sequences from mitochondrial and nuclear gene segments. On the basis of this clarified species‐level delimitation, we reassessed the geographical range of each Galictis taxon, identifying possible areas of sympatry between them. These results provide a solid taxonomic framework for Galictis, enabling the development of additional studies focusing on this poorly known taxon. © 2013 The Linnean Society of London, Zoological Journal of the Linnean Society, 2013, 167 , 449–472.     

Phylogeny and systematics of the Orycteropodidae (Mammalia,Tubulidentata)

The systematics of the order Tubulidentata is poorly known. Its phylogeny has never been thoroughly analysed and only a single review has ever been performed, which was over 30 years ago. This situation has hampered palaeoecological and palaeobiogeographical studies of these Neogene mammals. The present revision of the Orycteropodidae deals with the phylogeny and systematics of all African and Eurasian species over the last 20 Myr. The first comprehensive cladistic analysis of the family is presented here. The results of this analysis, based on 39 coded morphological characters, supplemented by non‐coded features taken from all over the skeleton, was used to reconstruct the phylogeny of the order Tubulidentata. Two distinct lineages within the genus Orycteropus are recognized and characterized. The new genus Amphiorycteropus is subsequently created, in order to harmonize taxonomy and phylogeny. The fossil genera Leptorycteropus and Myorycteropus are validated, bringing the number of genera in the order Tubulidentata to four. Moreover, within the family Orycteropodidae, the number of confirmed species is now 14. The outcome of this study allows us to propose a consistent palaeobiogeographical scenario for aardvarks. Finally, this revision represents the most comprehensive work on the evolutionary history of the order Tubulidentata to date, and provides a new framework for future studies. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 155 , 649–702.     

Adaptive radiation in miniature: the minute salamanders of the Mexican highlands (Amphibia: Plethodontidae: Thorius)

The small size and apparent external morphological similarity of the minute salamanders of the genus Thorius have long hindered evolutionary studies of the group. We estimate gene and species trees within the genus using mitochondrial and nuclear DNA from nearly all named and many candidate species and find three main clades. We use this phylogenetic hypothesis to examine patterns of morphological evolution and species coexistence across central and southern Mexico and to test alternative hypotheses of lineage divergence with and without ecomorphological divergence. Sympatric species differ in body size more than expected after accounting for phylogenetic relationship, and morphological traits show no significant phylogenetic signal. Sympatric species tend to differ in a combination of body size, presence or absence of maxillary teeth, and relative limb or tail length, even when they are close relatives. Sister species of Thorius tend to occupy climatically similar environments, which suggests that divergence across climatic gradients does not drive species formation in the genus. Rather than being an example of cryptic species formation, Thorius more closely resembles an adaptive radiation, with ecomorphological divergence that is bounded by organism‐level constraints. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109 , 622–643.     

A revision of Nereimyra (Psamathini,Hesionidae, Aciculata,Annelida)

Nereimyra Blainville, 1828 (Psamathini, Hesionidae, Aciculata, Annelida) is revised based on examination of all available types and newly collected specimens. We assessed the phylogeny of Nereimyra in an analysis based on cytochrome oxidase c subunit I (COI), 16S rDNA, 18S rDNA, and 28S rDNA. The genus is delineated to include the three species Nereimyra aphroditoides (Fabricius, 1780), Nereimyra punctata (O.F. Müller, 1776), and Nereimyra woodsholea (Hartman, 1965), which are redescribed. Nereimyra punctata has a characteristic pigmentation, but otherwise there are no clear morphological characters for separating the species. Based on the molecular data we obtained strong support both for the monophyly of Nereimyra and for each of the three included species. Nereimyra punctata and N. woodsholea are sister species, and the Kimura two‐parameter (K2P)‐corrected COI distances between the three species are 16–23%. Syllidia Quatrefages, 1866, is sister group to Nereimyra. Previous uncertainties regarding the type species of the genus are settled to Nereis rosea Fabricius, 1780, junior synonym of N. aphroditoides. A neotype is designated for N. aphroditoides. The distribution of Nereimyra is at present restricted to the Arctic and the boreal parts of the North Atlantic, possibly extending to the Gulf of Mexico on the United States east coast. Records outside this area require verification. Castalia multipapillata Théel, 1879, and Nereimyra alvinae Blake, 1985, are of uncertain affinity and are treated as nomina dubia. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 164 , 36–51.     

Two species of Haskinsia Grierson & Banks (Lycopsida) from the Middle Devonian of Xinjiang,China, and consideration of their palaeogeographical significance

Two species of the Devonian herbaceous lycopsid Haskinsia Grierson & Banks, H. hastata Berry & Edwards and H. sagittata Edwards & Benedetto, are reported from the Hujiersite Formation (Givetian–Middle Devonian), Xinjiang, north‐west China. Both species were first described from Venezuela. Haskinsia hastata from Xinjiang has hastate leaves with toothed margins, and a pair of basal narrow lateral segments which curve distally. It is assigned to a new subspecies because of the toothed margins which cannot be demonstrated in Venezuelan material. The scar of the sporangium stalk is observed for the first time in specimens of H. sagittata, on the leaves of which a possible ligule structure is also shown. On the basis of our observations on both Xinjiang and Venezuelan specimens, the diagnosis of Haskinsia is enlarged to accommodate plants whose lamina has entire or toothed margins. The palaeophytogeography of the genus, otherwise known from South and North America, is discussed. © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society, 2008, 157 , 633–644.