Is genome downsizing associated with diversification in polyploid lineages of Veronica?

The study of genome size evolution in a phylogenetic context in related polyploid and diploid lineages can help us to understand the advantages and disadvantages of genome size changes and their effect on diversification. Here, we contribute 199 new DNA sequences and a nearly threefold increase in genome size estimates in polyploid and diploid Veronica (Plantaginaceae) (to 128 species, c. 30% of the genus) to provide a comprehensive baseline to explore the effect of genome size changes. We reconstructed internal transcribed spacer (ITS) and trnL‐trnL‐trnF phylogenetic trees and performed phylogenetic generalized least squares (PGLS), ancestral character state reconstruction, molecular dating and diversification analyses. Veronica 1C‐values range from 0.26 to 3.19 pg. Life history is significantly correlated with 1C‐value, whereas ploidy and chromosome number are strongly correlated with both 1C‐ and 1Cx‐values. The estimated ancestral Veronica 1Cx‐value is 0.65 pg, with significant genome downsizing in the polyploid Southern Hemisphere subgenus Pseudoveronica and two Northern Hemisphere subgenera, and significant genome upsizing in two diploid subgenera. These genomic downsizing events are accompanied by increased diversification rates, but a ‘core shift’ was only detected in the rate of subgenus Pseudoveronica. Polyploidy is important in the evolution of the genus, and a link between genome downsizing and polyploid diversification and species radiations is hypothesized. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 178 , 243–266.     

Phylogenetic position and revised classification of Acacia s.l. (Fabaceae: Mimosoideae) in Africa,including new combinations in Vachellia and Senegalia

Previous phylogenetic studies have indicated that Acacia Miller s.l. is polyphyletic and in need of reclassification. A proposal to conserve the name Acacia for the larger Australian contingent of the genus (formerly subgenus Phyllodineae) resulted in the retypification of the genus with the Australian A. penninervis. However, Acacia s.l. comprises at least four additional distinct clades or genera, some still requiring formal taxonomic transfer of species. These include Vachellia (formerly subgenus Acacia), Senegalia (formerly subgenus Aculeiferum), Acaciella (formerly subgenus Aculeiferum section Filicinae) and Mariosousa (formerly the A. coulteri group). In light of this fragmentation of Acacia s.l., there is a need to assess relationships of the non‐Australian taxa. A molecular phylogenetic study of Acacia s.l and close relatives occurring in Africa was conducted using sequence data from matK/trnK, trnL‐trnF and psbA‐trnH with the aim of determining the placement of the African species in the new generic system. The results reinforce the inevitability of recognizing segregate genera for Acacia s.l. and new combinations for the African species in Senegalia and Vachellia are formalized. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 172 , 500–523.     

Phylogeographic analyses reveal distinct lineages of the liverworts Metzgeria furcata (L.) Dumort. and Metzgeria conjugata Lindb. (Metzgeriaceae) in Europe and North America

Seed plant genera often exhibit intercontinental disjunctions where different species are found on different continents. Many morphologically circumscribed bryophyte species exhibit similar disjunctions. We used nucleotide sequences from the plastid and nuclear genomes to test hypotheses of phylogeography within representatives of the genus Metzgeria: Metzgeria furcata, Metzgeria conjugata, and Metzgeria myriopoda. The first two species have sexual and asexual populations, exhibit disjunctions between North America and Europe, and have been split into separate species, numerous subspecies or varieties. The third species occurs in eastern North America but is not reported from Europe. Phylogenetic analyses resolved three distinct lineages within the morphologically defined species, M. furcata: one in North America, and two in Europe. Similarly, three morphologically cryptic clades of M. conjugata were resolved by the molecular data: northern North America, Europe, and south‐eastern North America. For both species, molecular divergence among taxa occurred in the absence of morphological change. In the case of M. myriopoda, all plants from eastern North America were both morphologically uniform and genetically homogeneous (although not identical). The present study provides significant insight into a plant group with complex taxonomy, and indicates that these liverwort taxa with wide distributions, extreme sex ratios, and continental disjunctions harbor cryptic lineages. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 98 , 745–756.     

Karyology of the genus Epidendrum (Orchidaceae: Laeliinae) with emphasis on subgenus Amphiglottium and chromosome number variability in Epidendrum secundum

Epidendrum is one of the largest Neotropical genera of Orchidaceae and comprises approximately 1500 species. Only 2.8% of these species have been studied cytologically, demonstrating chromosome numbers ranging from n = 12 in E. fulgens to n = 120 in E. cinnabarinum. The present work evaluated the evolution of the karyotypes of Epidendrum spp. based on data gathered from the literature and from analyses of the karyotypes of 16 Brazilian species (nine previously unpublished). The appearance of one karyotype with n = 12 with one larger chromosome pair in subgenus Amphiglottium appears to have occurred at the beginning of the divergence of this lineage, and x = 12 probably represents the basic number of this subgenus. Epidendrum secundum exhibits wide variation in chromosome numbers, with ten different cytotypes found in 22 Brazilian populations, seven of which were new counts: 2n = 30, 42, 50, 54, 56, 58 and 84. Most lineages of Epidendrum seem to have been secondarily derived from one ancestral stock with x = 20, as is seen in the majority of the present‐day representatives of the genus. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 172 , 329–344.     

Hidden diversity of Euscorpius (Scorpiones: Euscorpiidae) in Greece revealed by multilocus species‐delimitation approaches

Phylogenetic analysis of the genus Euscorpius (Scorpiones: Euscorpiidae) across the Mediterranean region (86 specimens, 77 localities, four DNA markers: 16S rDNA, COI, COII, and ITS1), focusing on Greek fauna, revealed high variation, deep clade divergences, many cryptic lineages, paraphyly at subgenus level, and sympatry of several new and formerly known lineages. Numerous specimens from mainland and insular Greece, undoubtedly the least studied region of the genus' distribution, have been included. The reconstructed phylogeny covers representative taxa and populations across the entire genus of Euscorpius. The deepest clades detected within Euscorpius correspond (partially) to its current subgeneric division, outlining subgenera Tetratrichobothrius and Alpiscorpius. The rest of the genus falls into several clades, including subgenus Polytrichobothrius and a paraphyletic subgenus Euscorpius s.s. Several cryptic lineages are recovered, especially on the islands. The inadequacy of the morphological characters used in the taxonomy of the genus to delineate species is discussed. Finally, the time frame of differentiation of Euscorpius in the study region is estimated and the distributional patterns of the lineages are contrasted with those of other highly diversified invertebrate genera occurring in the study region. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 110 , 728–748.     

Divergence in the shell morphology of the land snail genus Aegista (Pulmonata: Bradybaenidae) under phylogenetic constraints

The role of natural selection in phenotypic evolution is central to evolutionary biology. Phenotypic evolution is affected by various factors other than adaptation, and recent focus has been placed on the effects of phylogenetic constraints and niche conservatism on phenotypic evolution. Here, we investigate the relationship between the shell morphology and habitat use of bradybaenid land snails of the genus Aegista and clarify the causes of the divergence in shell morphology among phylogenetically related species. The results of ancestral state reconstruction showed that arboreal species have evolved independently from ground‐dwelling species at least four times. A significant association was found between shell shape and habitat use, despite the existence of a certain degree of phylogenetic constraint between these traits. A principal component analysis showed that arboreal species tend to have a relatively high‐spired shell with a narrow umbilicus. By contrast, ground‐dwelling species have a low‐spired shell with a wide umbilicus. Although the latitude and elevation of the sampling locations showed no relationship with shell morphology, the geology of the sampling locations affected the shell size of arboreal species. The development of a well‐balanced shell shape is one effective method for reducing the cost of locomotion under the force of gravity in each life habitat, resulting in the divergence in shell morphology and the independent evolution of morphologically similar species among different lineages. The present study suggests that ecological divergence is probably the cause of shell morphology divergence in land snails. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 114 , 229–241.     

Testing concordance in species boundaries using acoustic,morphological, and molecular data in the field cricket genus Itaropsis (Orthoptera: Grylloidea,Gryllidae: Gryllinae)

In most taxa, species boundaries are inferred based on differences in morphology or DNA sequences revealed by taxonomic or phylogenetic analyses. In crickets, acoustic mating signals or calling songs have species‐specific structures and provide a third data set to infer species boundaries. We examined the concordance in species boundaries obtained using acoustic, morphological, and molecular data sets in the field cricket genus Itaropsis. This genus is currently described by only one valid species, Itaropsis tenella, with a broad distribution in western peninsular India and Sri Lanka. Calling songs of males sampled from four sites in peninsular India exhibited significant differences in a number of call features, suggesting the existence of multiple species. Cluster analysis of the acoustic data, molecular phylogenetic analyses, and phylogenetic analyses combining all data sets suggested the existence of three clades. Whatever the differences in calling signals, no full congruence was obtained between all the data sets, even though the resultant lineages were largely concordant with the acoustic clusters. The genus Itaropsis could thus be represented by three morphologically cryptic incipient species in peninsular India; their distributions are congruent with usual patterns of endemism in the Western Ghats, India. Song evolution is analysed through the divergence in syllable period, syllable and call duration, and dominant frequency. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 164 , 285–303.     

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.     

The early evolution of the mega‐diverse genus Begonia (Begoniaceae) inferred from organelle DNA phylogenies

Begonia L. is one of the largest flowering plant genera, a ubiquitous component of many tropical forests and an economically important ornamental plant. In the present study, we address the early evolution of Begonia by generating molecular phylogenies from approximately 7000 bases of chloroplast DNA and approximately 6000 bases of mitochondrial DNA for each of 30 exemplar Begonia species. Broadscale biogeographic patterns found in the phylogenies, together with previously estimated divergence dates, indicated that extant Begonia lineages first diversified in Africa and then subsequently in America and Asia. The phylogenies also revealed that the closest African relatives of the American and Asian Begonia are seasonally‐adapted species. Moderate to strong incongruence between the phylogenies suggested that they differ genealogically. These differences could have been the result of either interspecific hybridization and/or incomplete lineage sorting. The results obtained in the present study provide a much needed genus‐wide framework for future evolutionary studies of this exceptionally diverse tropical genus. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 101 , 243–250.     

A new species of Daphniopsis (Crustacea: Anomopoda: Daphniidae) from Australian salt lakes

A new species of the genus Daphniopsis found in Australian salt lakes is described and illustrated. A differential diagnosis and short taxonomic remarks are presented.     

Phylogeography of the whelk genus Cominella (Gastropoda: Buccinidae) suggests long‐distance counter‐current dispersal of a direct developer

The gastropod genus Cominella Gray, 1850 consists of approximately 20 species that inhabit a wide range of marine environments in New Zealand and Australia, including its external territory, the geographically isolated Norfolk Island. This distribution is puzzling, however, with apparently closely‐related species occurring either side of the Tasman Sea, even though all species are considered to have limited dispersal abilities. To determine how Cominella attained its current distribution, we derived a dated molecular phylogeny, which revealed a clade comprising all the Australian and Norfolk Island species nested within four clades of solely New Zealand species. This Australian clade diverged well after the vicariant separation of New Zealand from Australia, and implies two long‐distance dispersal events: a counter‐current movement across the Tasman Sea from New Zealand to Australia, occurring at the origination of the clade, followed by the colonization of Norfolk Island. The biology of Cominella suggests that the most likely method of long‐distance dispersal is rafting as egg capsules. Our robust phylogeny also means that the current Cominella classification requires revision. We propose that our clades be recognized as subgenera: Cominella (s.s.), Cominista, Josepha, Cominula, and Eucominia, with each subgenus comprising only of New Zealand or Australian species. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 115 , 315–332.     

Phylogeography of two cryptic species of African desert jerboas (Dipodidae: Jaculus)

The lesser Egyptian jerboa Jaculus jaculus is a desert dwelling rodent that inhabits a broad Arabian–Saharan arid zone. Recently, two distant sympatric lineages were described in North‐West Africa, based on morphometric and molecular data, which may correspond to two cryptic species. In the current study, phylogenetic relationships and phylogeographical structure among those lineages and geographical populations from North Africa and the Middle East were investigated. The phylogeographical patterns and genetic diversity of the cytochrome b gene (1110 bp) were addressed on 111 jerboas from 41 localities. We found that the variation in Africa is partitioned into two divergent mitochondrial clades (10.5% divergence relating to 1.65–4.92 Mya) that corresponds to the two cryptic species: J. jaculus and J. deserti. Diversifications within those cryptic species/clades were dated to 0.23–1.13 Mya, suggesting that the Middle Pleistocene climatic change and its environmental consequences affected the evolutionary history of African jerboas. The third distant clade detected, found in the Middle East region, most likely represents a distinct evolutionary unit, independent of the two African lineages. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ??, ??–??.     

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

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

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.     

Species diversity of the deep‐water gulper sharks (Squaliformes: Centrophoridae: Centrophorus) in North Atlantic waters – current status and taxonomic issues

The gulper sharks (genus Centrophorus) are a group of deep‐water benthopelagic sharks with a worldwide distribution. The alpha taxonomy of the group has historically been problematic and the number of species included in the genus has varied considerably over the years and is still under debate. Gulper sharks are routinely caught in mid‐ and deep‐water fisheries worldwide and some have shown a considerable decline in abundance in the last few decades. Clear and consistent species discrimination of Centrophorus is essential for an efficient and sustainable management of these fisheries resources. Our study used molecular cytochrome oxidase subunit I (COI) and 16S ribosomal RNA gene sequences and morphometric data to re‐evaluate the diversity of Centrophorus in North Atlantic waters, including the Gulf of Mexico, the Caribbean, and the Mediterranean Seas. Molecular data separated North Atlantic Centrophorus into five well‐supported groups whereas morphometric data separated these same five groups and suggested three additional groups for which no molecular data were available. Four of the five groups identified in the North Atlantic also occur in the Indian and/or Pacific Oceans, thus extending the reported range of some species considerably. A species identification key for North Atlantic Centrophorus is provided based on our findings. © 2014 The Linnean Society of London     

Molecular phylogeny of the subgenus Holothuria (Selenkothuria) Deichmann, 1958 (Holothuroidea: Aspidochirotida)

The subgenus Selenkothuria comprises 12 species of tropical shallow water sea cucumbers that share morphological features, such as rods in the body wall and tube feet, modified tentacles for suspension feeding, and cryptic colours. The taxonomic status of this taxon has been controversial, but currently it is accepted as a subgenus of the genus Holothuria. Phylogenetic analyses of mitochondrial genes [cytochrome c oxidase subunit 1 (COI), 16S RNA] of ten species of Selenkothuria and related subgenera showed the polyphyly of this subgenus; monophyly was rejected by a likelihood ratio test. A geographical split divides the species of this subgenus into three different groups: one Indo‐West‐Pacific (IWP) group and two American groups. The IWP group is more closely related to Holothuria (Semperothuria) cinerascens and to other subgenera such as Roweothuria, Holothuria, and Vaneyothuria, whereas the two American groups are more closely related to each other and to some species of the subgenus Halodeima. These results suggest multiple parallel originations and diversification of ossicle morphology within the subgenus Selenkothuria. The current scheme of subgenera for the genus Holothuria is not supported, suggesting the need for a new classification. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 165 , 109–120.     

Phylogenetic analysis of eastern Asian and eastern North American disjunct Lespedeza (Fabaceae) inferred from nuclear ribosomal ITS and plastid region sequences

Lespedeza (tribe Desmodieae, Fabaceae) follows a disjunct distribution in eastern Asia and eastern North America. Phylogenetic relationships among its species and related taxa were inferred from nuclear ribosomal internal transcribed spacer (ITS) and plastid sequences (trnH‐psbA, psbK‐psbI, trnK‐matK and rpoC1). We examined 35 species of Lespedeza, two of Kummerowia and one of Campylotropis, the sole constituents of the Lespedeza group. An analysis of these data revealed that the genus Campylotropis is sister to the other two genera. However, we were unable to resolve the relationships between Kummerowia and Lespedeza in the strict consensus trees of parsimony analyses based on plastid and combined DNA data. In the genus Lespedeza, the Old World subgenus Macrolespedeza is monophyletic, whereas the transcontinental subgenus Lespedeza is paraphyletic. Monophyly of eastern Asian species and of North American species is strongly supported. Although inconsistent with the traditional classification, this phylogenetic finding is consistent with seedling morphology. Three subgroups recognized in subgenus Macrolespedeza were unresolved in our phylogenetic trees. An incongruence length difference (ILD) test indicated that the two partitions (nuclear ITS and plastid sequences) were significantly incongruent, perhaps because of hybridization between species in Lespedeza. Most of the primary clades of tribe Desmodieae are Asian, implying that the relatively few New World ones, such as those in Lespedeza, are more recently derived from Asia. © 2010 The Linnean Society of London, Botanical Journal of the Linnean Society, 2010, 164 , 221–235.     

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.