The systematic value of pollen morphology in Smilacaceae

Smilacaceae are a small family of dioecious, mostly climbing, net-veined monocotyledons with a cosmopolitan distribution. Relatively little is known about the variation of pollen morphology within the family. For this reason, and to investigate the systematic value of palynology in Smilacaceae, pollen from 125 species of Smilax, Heterosmilax, and Ripogonum was examined using light and scanning electron microscopy. Ten of these were examined further by transmission electron microscopy. Four distinct pollen types grouped into two major pollen classes were distinguished: Class 1, represented by the pollen of all Smilax and Heterosmilax species, is mostly spheroidal, inaperturate, and spinulate or microspinulate, with a thin, fragile exine of varied sculpturing; three pollen types are represented within this class. Class 2 is found only in Ripogonum and contains a single pollen type with prolate, monosulcate, reticulately-sculptured pollen. The unique pollen morphology of Ripogonum supports its removal from Smilacaceae. In contrast, the characteristics of Heterosmilax pollen intergrade with those seen in Smilax, suggesting that the former might be better reduced to synonymy with the latter. A key to the identification of these pollen types is presented along with a discussion of geographic and possible evolutionary trends among them.     

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.     

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 taxonomic revision of the genus Heterosmilax (Smilacaceae)

Heterosmilax, a small southeastern Asiatic genus in the Smilacaceae, comprises 11 species in two sections, includingH. micrandra, which is described as new from Hainan, China. These taxa are taxonomically discussed, described, illustrated, and a key is provided to differentiate them.     

Morphological and molecular description of new species of squat lobster (Crustacea: Decapoda: Galatheidae) from the Solomon and Fiji Islands (South‐West Pacific)

The family Galatheidae is among the most diverse families of anomuran decapod crustaceans, and the South‐West Pacific is a biodiversity hot spot for these squat lobsters. Attempts to clarify the taxonomic and evolutionary relationships of the Galatheidae on the basis of morphological and molecular data have revealed the existence of several cryptic species, differentiated only by subtle morphological characters. Despite these efforts, however, relationships among genera are poorly understood, and the family is in need of a detailed systematic review. In this study, we assess material collected in different surveys conducted in the Solomon Islands, as well as comparative material from the Fiji Islands, by examining both the morphology of the specimens and two mitochondrial markers (cytochrome oxidase subunit I, COI, and 16S rRNA). These two sources of data revealed the existence of eight new species of squat lobster, four of which were ascribed to the genus Munida, two to the genus Paramunida, one to the genus Plesionida, and the last species was ascribed to the genus Agononida. These eight species are described along with phylogenetic relationships at the genus level. Our findings support the taxonomic status of the new species, yet the phylogenetic relationships are not yet fully resolved. Further molecular analysis of a larger data set of species, and more conserved genes, will help clarify the systematics of this group. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 156 , 465–493.     

Phylogeny and evolution of the South African genus Metalasia (Asteraceae–Gnaphalieae) inferred from molecular and morphological data

Metalasia is a genus in tribe Gnaphalieae (Asteraceae), endemic to South Africa and with its main distribution in the Cape Floristic Region. The genus comprises 57 species and, with a number of closely related genera, it constitutes the ‘Metalasia clade’. A species‐level phylogenetic analysis is presented, based on DNA sequences from two nuclear (internal and external transcribed spacer: ITS, ETS) and two plastid (psbA‐trnH, trnL‐trnF) regions together with morphological data. Analyses combining molecular and morphological data attempt not only to resolve species interrelationships, but also to detect patterns in character evolution. Phylogenetic analyses corroborate our earlier study and demonstrate that Metalasia is formed of two equally sized, well‐supported sister groups, one of which is characterized by papillose cypselas. The results differ greatly from earlier hypotheses based on morphology alone, as few morphological characters support the phylogenetic patterns obtained. The two clades of Metalasia do, however, appear to differ in distribution, corresponding to the different rainfall regimes of South Africa. Analyses show a few taxa to be problematic; one example is the widely distributed M. densa which appears to be an intricate species complex. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 174 , 173–198.     

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.     

Molecular phylogenetics,character evolution and systematics of the genus Micranthes (Saxifragaceae)

With c. 85 species, the genus Micranthes is among the larger genera of the Saxifragaceae. It is only distantly related to the morphologically similar genus Saxifraga, in which it has frequently been included as Saxifraga section Micranthes. To study the molecular evolution of Micranthes, we analysed nuclear ribosomal (internal transcribed spacer, ITS) and plastid (trnL–trnF) DNA sequences in a comprehensive set of taxa comprising c. 75% of the species. The molecular phylogenetic tree from the combined dataset revealed eight well‐supported clades of Micranthes. These clades agree in part with previously acknowledged subsections or series of Saxifraga section Micranthes. As these eight groups can also be delineated morphologically, we suggest that they should be recognized as sections of Micranthes. New relationships were also detected for some species and species groups, e.g. section Davuricae sister to sections Intermediae and Merkianae, and M. micranthidifolia as a member of section Micranthes. Species proposed to be excluded from the genus Micranthes for morphological reasons were resolved in the molecular tree in Saxifraga. Many morphological characters surveyed were homoplasious to varying extents. Micromorphological characters support comparatively well the clades in the phylogenetic tree. An updated nomenclature and a taxonomic conspectus of sections and species of Micranthes are provided. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 178 , 47–66.     

Phylogenetic relationships of Mexican minnows of the genus Notropis (Actinopterygii, Cyprinidae)

We conducted phylogenetic analyses based on complete mitochondrial cytochrome b gene sequences among southern and central Mexican cyprinid species, included in the genera Notropis and Hybopsis. In addition 15 northern species of the genera Notropis and Hybopsis were included in the analyses in order to place the Mexican species into a larger phylogenetic framework. The phylogenetic relationships supported the existence of five major clades: (1) including species of the subgenus Alburnops of the genus Notropis plus N. shumardi; (2) species of the subgenus Notropis; (3) species of the genus Hybopsis; (4) species of the N. texanus + N. volucellus species group of the genus Notropis; (5) Mexican endemic species of the genus Notropis plus the genus Yuriria. Previous phylogenetic inferences based on morphological characters resolved the Mexican minnows analysed as N. sallaei, N. calientis, N. boucardi and Y. alta, non‐monophyletic. According to our cytochrome b evidence all Mexican minnows of the genera Notropis and Yuriria formed a monophyletic group with respect to the northern species of the genera Notropis and Hybopsis. Within the Mexican clade, three well‐supported clades were identified: the first included the closely related species N. moralesi and N. boucardi, which occur in three independent drainages of south Mexico; the second consisted of two different lineages, N. imeldae and an undescribed species of Notropis, inhabiting two independent drainages of south Mexico; the third comprised two central Mexican Notropis species (N. calientis and N. sallaei) and the Y. alta populations. Based on this study and pending a more extensive taxonomic revision of the genus Notropis, we adopt the conservative criterion of considering all Notropis species from southern and central Mexico examined, including Y. alta, as belonging to the genus Notropis. © 2003 The Linnean Society of London, Biological Journal of the Linnean Society, 2003, 80 , 323–337.     

The diversification of the genus Monodelphis and the chronology of Didelphidae (Didelphimorphia)

To evaluate the monophyletic status of the genus Monodelphis, and its species complexes, we used a 9.3‐kb multimarker alignment to build a phylogenetic tree based on the largest taxon sampling for this didelphid genus to date. Furthermore, using a Bayesian framework and six calibration points, we inferred the divergence times for the major Monodelphis lineages and their current geographical distribution to perform an ancestral state reconstruction for geographical areas. Our results indicate the monophyletic nature of Monodelphis and suggest ‘kunsi’ as a new species complex that includes Monodelphis kunsi and an undescribed species. Monodelphis is further subdivided into three clades showing a common vicariance pattern, with each major clade consisting of a northern South American lineage joined with an Atlantic Forest lineage. This geographic consistency suggests a vicariant event that might have been related to a warm period at the Oligocene/Miocene border, according to our time results. © 2015 The Linnean Society of London     

Molecular phylogenetics and biogeography of the eastern Asian–eastern North American disjunct Mitchella and its close relative Damnacanthus (Rubiaceae,Mitchelleae)

Mitchella is a small genus of the Rubiaceae with only two species. It is the only herbaceous semishrub of the family showing a disjunct distribution in eastern Asia and eastern North America, extending to Central America. Its phylogeny and biogeographical diversification remain poorly understood. In this study, we conducted phylogenetic and biogeographical analyses for Mitchella and its close relative Damnacanthus based on sequences of the nuclear internal transcribed spacer (ITS) and four plastid markers (rbcL, atpB‐rbcL, rps16 and trnL‐F). Mitchella is monophyletic, consisting of an eastern Asian M. undulata clade and a New World M. repens clade. Our results also support Michella as the closest relative to the eastern Asian Damnacanthus. The divergence time between the two intercontinental disjunct Mitchella species was dated to 7.73 Mya, with a 95% highest posterior density (HPD) of 3.14?12.53 Mya, using the Bayesian relaxed clock estimation. Ancestral area reconstructions suggest that the genus originated in eastern Asia. The semishrub Mitchella appears to have arisen from its woody ancestor in eastern Asia and then migrated to North America via the Bering land bridge in the late Miocene. © 2013 The Linnean Society of London     

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.     

Testing the monophyly and position of the North American shrubby desert genus Leucophyllum (Scrophulariaceae: Leucophylleae)

Leucophyllum is one of the most remarkable endemic genera of North American deserts, with its simultaneous bloom of showy purple flowers. With Eremogeton and probably Capraria it forms part of tribe Leucophylleae. Leucophyllum has 16 species distributed mostly throughout the Chihuahuan and Tehuacán deserts. The three genera were sampled to investigate the phylogenetic relationships among them and to test the monophyly of Leucophyllum, based on plastid DNA (trnL‐F, rps16) and nuclear ribosomal (nr)DNA (internal transcribed spacer) sequences. Bayesian inference and maximum‐likelihood analyses confirmed that tribe Leucophylleae is monophyletic and formed by the three Neotropical genera. Separate (plastid DNA and nrDNA) and combined analyses retrieved Leucophyllum as paraphyletic, with L. mojinense as the sister species to the rest of the species in the tribe and Capraria spp. nested in one of two clades of Leucophyllum. Further monographic work is needed to identify the defining characters and limits of the genera, but we suggest that L. mojinense, with its different vegetative architecture, distinctive flowers and dissimilar distribution could be placed in its own genus. Each of the two clades in Leucophyllum could be considered a genus in its own right, and Capraria and Eremogeton can be recognized as independent genera, as they are at present. Leucophyllum ambiguum, the type species of the genus, belongs to one of the clades so the species of the other could be considered members of a new genus. The only diagnostic character detected at present is a ventricose corolla tube in one of the clades in Leucophyllum and a pressed corolla tube in the other. © 2013 The Linnean Society of London     

Phylogenetic signal in the evolution of body colour and spicule skeleton in calcareous sponges

Some of the morphological characters used in Porifera taxonomy have often been shown to be inconsistent. In the present study, we tested the phylogenetic coherence of currently used taxonomic characters of the calcarean genus Clathrina. For this, 20 species of Clathrina and three other calcinean genera (Ascandra, Guancha, and Leucetta) were sequenced for the ITS and D2 region of the 28S ribosomal DNA. Maximum‐likelihood and maximum‐parsimony algorithms were used to reconstruct phylogenetic trees. Deep divergences were observed in our tree and Clathrina was shown to be paraphyletic. The major split in our topology showed a clear‐cut distinction between sponges with and without tetractine spicules. Moreover, a group of yellow‐coloured Clathrina was clearly separated from the remaining white‐coloured species. Our results show that the presence of diactines, water‐collecting tubes, the degree of cormus anastomosis, and actine shapes do not correlate with the major clades of the calcinean phylogeny. On the other hand, the presence of tripods, the absence of tetractines, and the presence of spines in the apical actine of tetractines seem to be good synapomorphies for clades in our tree. Our results demonstrate that skeleton characters can be reliably used in higher level taxonomy in Clathrinida. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 163 , 1026–1034.     

A combined morphological and molecular phylogenetic analysis of Parthenocissus (Vitaceae) and taxonomic implications

Parthenocissus (the Virginia creeper genus, Vitaceae) consists of 13 species and shows a disjunct distribution between Asia and North America. We investigated the inflorescence structure, calyx morphology, appendages on the inner side of petals, leaf epidermis, pollen and seed characters throughout the genus. A combined phylogenetic analysis with 27 morphological and 4137 molecular characters was conducted and the result was largely congruent with that of the previous molecular work, but with higher resolution. The combined analysis identified two clades corresponding to the Asian and North American taxa. Parthenocissus feddei was resolved as closely related to the clade containing P. cuspidifera, P. heterophylla and P. semicordata. The four species share synapomorphies of having conspicuously raised veinlets, an obscurely five‐ (to eight‐) lobed calyx, appendages on the inner side of petals covering the entire length of anthers and foveolate pollen exine ornamentation. Within the Old World clade, the pentafoliolate species were weakly supported as more closely related to species with both simple and trifoliolate leaves. Furthermore, the ancestral states of tendril apices, inflorescence structure, appendages on the inner side of petals and exine ornamentation of pollen grains were reconstructed on the molecular strict consensus tree. The appendages on the inner side of petals and exine ornamentation of pollen grains were suggested to be important characters in the taxonomy of Parthenocissus, especially for species with trifoliolate leaves. Finally, the previous classifications of Parthenocissus were evaluated within the phylogenetic framework. © 2011 The Linnean Society of London, Botanical Journal of the Linnean Society, 2011, ?? , ??–??.     

Molecular phylogenetic analysis of Podostemaceae: implications for taxonomy of major groups

The river‐weed family Podostemaceae (c. 300 species in c. 54 genera) shows a number of morphological innovations to be adapted to its unusual aquatic habitat, and its unique or rare bauplan features have been reflected in the traditional (i.e. non‐molecular) classification recognizing numerous monotypic or oligospecific genera. The infrasubfamilial relationships of many genera remained unclear. The present study used molecular phylogenetic analysis of matK sequences for 657 samples (c. 132 species/c. 43 genera). The family was traditionally divided into three subfamilies (Podostemoideae, Tristichoideae and Weddellinoideae). American Podostemoideae were shown to be polyphyletic and divided into four clades, i.e. Ceratolacis, Diamantina, Podostemum and all other genera. Among the podostemoid clades, Diamantina was the first branching clade and a clade comprising Mourera and the Apinagia subclade was then sister to the remainder of the New World and Old World Podostemoideae with low statistic supports. The Old World Podostemoideae comprised four monophyletic clades, i.e. two African clades, one Madagascan clade and one Asian clade, although the relationships among these clades and American Ceratolacis and Podostemum were poorly resolved. African Podostemoideae were polyphyletic, with Saxicolella pro parte being weakly supported as sister to the remaining Old World Podostemoideae plus Ceratolacis and Podostemum. In contrast to the American and African clades, monophyly of four Asian subclades was well supported. Plants of Tristicha (Tristichoideae) and of Weddellina (Weddellinoideae), which are currently treated as monospecific, had great matK differentiation equivalent to at least interspecific variation. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 169 , 461–492.     

啄木鸟科内谱系生物地理学新探

啄木鸟群体共包含254种,但早期对啄木鸟的分类学研究局限于形态学、行为学和鸣唱法等方向,分子研究结果又彼此存在差异,因此啄木鸟分类系统目前还有争议。分子数据的大量累积为啄木鸟系统发育的研究提供了条件。利用从GenBank获取的ND2基因序列,对啄木鸟科179种啄木鸟采用NJ法、MP法以及ML法分别进行了分子进化树构建,同时用NJ法重建了Picumnus属分子进化树。此外又利用cytb基因序列采用NJ法对Dryobates属和Picoides属进行分子进化树重建。我们的结果显示,姬啄木亚科Picumnus属新大陆物种彼此的进化关系仍需进一步研究,而该属唯一一种旧大陆种P.innominatus,种内遗传差异在种间水平依然显著,这说明其种内遗传差异一直被低估了。在啄木鸟亚科内,Hemicircus属和Nesoctites属为姐妹关系,而Geocolaptes olivaceus插入了Campethera属支系中,并非与其构成姐妹群体。此外,一些姐妹群在新旧大陆上的分布,推测这种分布可能与第四纪冰川有关。啄木鸟从旧大陆向新大陆迁移,在第四纪冰川作用下不断发生分布范围的扩张与收缩,最终形成现存的分布格局。     

The flightless marine midge Pontomyia (Diptera: Chironomidae): ecology,distribution, and molecular phylogeny

Pontomyia Edwards, 1926 (Diptera: Chironomidae) is a genus of exclusively marine flightless midges. There are four described species from the Indo‐Pacific, and one undescribed species known only from females, pupal skins, and larvae from the Atlantic/Caribbean. They are poorly known owing to their small size (～1.0 mm), extremely short adult life (< 3 h), and unusual habitat for an insect (coastal lagoons, bays, or rock pools). We reviewed scattered literature on their biology and systematics, presented photomicrographs of the male hypogium, and updated the geographic distribution of each species. We carried out the first molecular study to elucidate relationships among and within three of the species. Results from our four‐gene phylogenetic reconstruction using combined gene tree and species tree approaches showed that Pontomyia natans, Pontomyia oceana, and Pontomyia pacifica are each well‐supported clades, with P. natans as sister to P. oceana + P. pacifica. Genetic distances based on mitochondrial cytochrome oxidase I are extraordinarily large within P. natans and P. pacifica, which suggests that they may be cryptic species complexes. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 162 , 443–456.     

Increased molecular divergence of two endemic Trachelipus (Isopoda,Oniscidea) species from Greece reveals patterns not congruent with current taxonomy

In the present study, we employed three mitochondrial DNA genetic markers in a phylogenetic analysis aiming at the delineation of the relationships amongst nominal Trachelipus kytherensis populations, as well as between populations of this species and of Trachelipus aegaeus and a new form, occurring syntopically with the latter. Both the phylogenetic analysis and the genetic distances separating populations, show the presence of several distinct and well differentiated clades that undermine the monophyly of T. kytherensis. On the other hand, despite the insular distribution of T. aegaeus populations, their divergence is low and the monophyly of this taxon can be rescued by the inclusion of two more insular populations previously assigned to T. kytherensis. The patterns of genetic divergence among clades are only partially congruent with the geographic distribution of populations. The validity of taxonomic characters used so far in the genus appears to be questionable; therefore, a more comprehensive phylogenetic study at a population level is deemed necessary for understanding the divergence of Trachelipus lineages. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 95 , 361–370.     

Multilocus phylogeny of a cryptic radiation of Afrotropical long-fingered bats (Chiroptera,Miniopteridae)

The Old World bat family Miniopteridae comprises only the genus Miniopterus, which includes 20 currently recognized species from the Afrotropical realm and 15 species from Eurasia and Australasia. Since 2003, the number of recognized Miniopterus species has grown from 19 to 35, with most newly described species endemic to Madagascar and the Comoros Archipelago. We investigated genetic variation, phylogenetic relationships and clade membership in Miniopterus focusing on Afrotropical taxa. We generated mitochondrial cytochrome-b (cyt-b) and nuclear intron data (five genes) from 352 vouchered individuals collected at 78 georeferenced localities. Including 99 additional mitochondrial sequences from GenBank, we analysed a total of 25 recognized species. Mitochondrial genetic distances among cyt-b-supported clades averaged 9.3%, representing as many as five undescribed species. Multilocus coalescent delimitation strongly supported the genetic isolation of eight of nine tested unnamed clades. A large number of sampled clades in sub-Saharan Africa are distributed wholly or partly in East Africa (nine of 13 clades), suggesting that Miniopterus diversity has been grossly underestimated. Although 25 of 27 cyt-b and 23 of 25 nuclear gene tree lineages from the Afrotropics were strongly supported as monophyletic, a majority of deep nodes were poorly resolved in phylogenetic analyses. Long terminal branches subtending short backbone internodes in the phylogenetic analyses suggest a rapid radiation model of diversification. This hypothesis needs to be tested using more phylogenetically informative data.