Contrasting patterns of diversification in a bird family (Aves: Gruiformes: Rallidae) are revealed by analysis of geospatial distribution of species and phylogenetic diversity

Geospatial patterns in the distribution of regional biodiversity reflect the composite processes that underpin evolution: speciation, dispersal and extinction. The spatial distribution and phylogeny of a globally widespread and species rich bird family (Rallidae) were used to help assess the role of large‐scale biogeographical processes in diversity and diversification. Here, we examine how different geostatistical diversity metrics enhance our understanding of species distribution by linking occurrence records of rail species to corresponding species level phylogeny. Tropical regions and temperate zones contained a large proportion of rail species richness and phylogenetic diversity whilst small islands in Australian, Oceanian and Oriental regions held the highest weighted and phylogenetic endemism. Our results suggest that habitat connectivity and dispersal were important ecological features in rail evolution and distribution. Spatial isolation was a significant driver of diversification where islands in Oceania were centres of neo‐endemism with recent multiple and independent speciation events and could be considered as nurseries of biodiversity. Palaeo‐endemism was mostly associated with older stable regions, so despite extensive long distance range shifting these areas retain their own ancient and distinct character. Madagascar was the major area of palaeo‐endemism associated with the oldest rail lineages and could be considered a museum of rail diversity. This implies a mixture of processes determine the current distribution and diversity of rail clades with some areas dominated by recent ‘in situ’ speciation while others harbour old diversity with ecological traits that have stood the test of time.     

Niche divergence promotes rapid diversification of East African sky island white‐eyes (Aves: Zosteropidae)

The Eastern Afromontane biodiversity hotspot composed of highly fragmented forested highlands (sky islands) harbours exceptional diversity and endemicity, particularly within birds. To explain their elevated diversity within this region, models founded on niche conservatism have been offered, although detailed phylogeographic studies are limited to a few avian lineages. Here, we focus on the recent songbird genus Zosterops, represented by montane and lowland members, to test the roles of niche conservatism versus niche divergence in the diversification and colonization of East Africa's sky islands. The species‐rich white‐eyes are a typically homogeneous family with an exceptional colonizing ability, but in contrast to their diversity on oceanic islands, continental diversity is considered depauperate and has been largely neglected. Molecular phylogenetic analysis of ~140 taxa reveals extensive polyphyly among different montane populations of Z. poliogastrus. These larger endemic birds are shown to be more closely related to taxa with divergent habitat types, altitudinal distributions and dispersal abilities than they are to populations of restricted endemics that occur in neighbouring montane forest fragments. This repeated transition between lowland and highland habitats over time demonstrate that diversification of the focal group is explained by niche divergence. Our results also highlight an underestimation of diversity compared to morphological studies that has implications for their taxonomy and conservation. Molecular dating suggests that the spatially extensive African radiation arose exceptionally rapidly (1–2.5 Ma) during the fluctuating Plio‐Pleistocene climate, which may have provided the primary driver for lineage diversification.     

Molecular phylogeny of the endemic East African flightless grasshoppers Altiusambilla Jago, Usambilla (Sjöstedt) and Rhainopomma Jago (Orthoptera: Acridoidea: Lentulidae)

Abstract.  A molecular phylogeny of endemic flightless grasshoppers is presented for the three Lentulidae genera Altiusambilla Jago, 1981 , Usambilla Sjöstedt, 1909 and Rhainopomma Jago, 1981 based on DNA sequences (16S rRNA locus). Parsimony, distance and likelihood reconstructions were performed using different assumptions on sequence evolution. The generated phylogenies agree in almost all parts of the calculated trees and support the monophyly of the observed genera. It was shown that Usambilla and Rhainopomma are more closely related to each other, Altiusambilla being a separate clade. However, the investigated East African lentulid genera are clearly separated from South African taxa, underlining the monophyly of East African genera. Usambilla olivacea is re-established. Populations of Rhainopomma montanum from the Taita Hills of Kenya and from the West Usambara mountains of Tanzania are two separate species not closely related to each other. Rhainopomma samples from the North Pare mountains of Tanzania belong to a hitherto undescribed species.     

Diversity and diversification of Eumolpinae (Coleoptera: Chrysomelidae) in New Caledonia

Contemporary taxonomic work on New Caledonian Eumolpinae (Chrysomelidae) has revealed their high species richness in this Western Pacific biodiversity hotspot. To estimate total species richness in this community, we used rapid DNA‐based biodiversity assessment tools, exploring mtDNA diversity and phylogenetic structure in a sample of 840 specimens across the main island. Concordance of morphospecies delimitation with units delimited by phenetic and phylogenetic algorithms revealed some 98–110 species in our sample, twice as many as currently described. Sample‐based rarefaction curves and species estimators using these species counts doubled this figure (up to 210 species), a realistic estimate considering taxonomic coverage, local endemism, and characteristics of sampling design, amongst others. New Caledonia, compared with larger tropical islands, stands out as a hotspot for Eumolpinae biodiversity. Molecular dating using either chrysomelid specific rates or tree calibration using palaeogeographical data dated the root of the ingroup tree (not necessarily a monophyletic radiation) at 38.5 Mya, implying colonizations after the Cretaceous breakage of Gondwana. Our data are compatible with the slowdown in diversification rates through time and are also consistent with recent faunal origins, possibly reflecting niche occupancy after an initial rapid diversification. Environmental factors (e.g. soil characteristics) seemingly played a role in this diversification process. © 2013 The Linnean Society of London     

A complex biogeographic history of diversification in Neotropical lancehead pitvipers (Serpentes,Viperidae)

Based on the literature, we had predicted that the diversification within the Neotropical snake genus Bothrops occurred along a latitudinal gradient from north to south, with diversification into unoccupied niches through ecological opportunity, not correlated with geoclimatic events. Using a dated phylogeny and estimating likelihoods of ancestral states at cladogenesis events, we reconstructed ancestral areas and assessed major events of the diversification of Bothrops clades, and we also discuss systematic implications for this group. Based on the phylogeny we produced, B. lojanus was not considered as part of the genus Bothrops since the results recovered this species nested within the Bothrocophias clade. We infer that the diversification of the Miocene Bothrops pictus and Bothrops alternatus clades may be related to the uplift of the western slopes of the Andes and the Argentinian Patagonian Andes, respectively. The Pliocene Bothrops taeniatus and Bothrops osbornei clades may be related to the uplift of the eastern and northern Andes, respectively. The Plio-Pleistocene Bothrops neuwiedi clade may be related to the habitat transitions from a warmer and forested environment to a cooler and open landscape; the Bothrops jararaca (i.e. island endemic species) and Bothrops lanceolatus clades to over-water dispersal with island speciation; and Bothrops atrox clade to the appearance of the Panamanian land bridge. We found that a multitemporal and multidirectional history of diversification may be correlated with geoclimatic and dispersalist events. We argue that the vacant niche hypothesis by itself does not explain Bothrops diversification.     

Patterns of diversification on old volcanic islands as revealed by the woodlouse-hunter spider genus Dysdera (Araneae, Dysderidae) in the eastern Canary Islands

Long-term erosion and subsidence cause dramatic alterations in the physical and ecological features of oceanic islands. Although oceanic islands have been extensively used as models for the study of speciation, little attention has been given to investigating evolutionary patterns in old volcanic islands that have suffered severe climatic degradation. The spider genus Dysdera has diversified across the Canary Islands and has evolved endemisms in the low-elevation, xeric eastern islands, which sharply contrast with the younger, higher, and more humid western islands. A combined phylogenetic analysis of seven mitochondrial and nuclear genes reveals that the eastern Canaries were colonized twice, although only one lineage underwent in situ diversification. Origins of the speciose lineage remain obscure, but probably preceded diversification of present-day Iberian and North African species. A second colonization of the eastern Canaries from North Africa has occurred in more recent times. Molecular analyses reveal several instances of geographically coherent cryptic lineages further supported by morphometric evidence. Analyses of diversification rates suggest deceleration of diversification over the course of time, and this is compatible with increasing extinction rates due to drastic yet continuous ecological changes. Extinction may also explain incongruent patterns of morphological differentiation and species coexistence. Despite a general trend towards community impoverishment, there is also evidence for recent speciation events linked to ecological shifts, which may illustrate the origins of nonspeciose relic lineages on islands.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 94 , 589–615.     

Extremely divergent song types in the genus Aerotegmina Hemp (Orthoptera: Tettigoniidae: Hexacentrinae) and the description of a new species from the Eastern Arc Mountains of Tanzania (East Africa)

The genus Aerotegmina comprises a group of African canopy-dwelling, predatory bushcrickets (katydids) that is known for its inflated tegmina and the unusually loud and low-frequency calling song of its type species. Here, we describe the songs of another two species of the genus which are much larger than the type species and have an even lower peak frequency. In addition, small and large species differ in song structure. While the type species and closely related forms have a broad banded, multi-peak song with strong components in the audio and ultrasonic range, the species treated here have an extremely narrow banded, resonant song with a carrier frequency of 2 kHz. With Q-values above 100 these sounds belong to the purest songs ever recorded in Orthoptera. Besides describing songs, stridulatory organs and a new species we discuss the possible functions of the song type. A key to the species of Aerotegmina is provided.     

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

The desert biota is exposed to extreme and variable conditions that shape its evolution and diversification processes. In this respect, the Jaculus jerboas have gained the attention of researchers as a result of their broad Saharan–Arabian distribution and their high and unexplained, morphological, anatomical, and molecular variation. In the present study, mitochondrial and nuclear genealogies where used to confirm monophyly of two cryptic species: Jaculus jaculus and Jaculus deserti. The reconstructed demography showed that the evolutionary histories of the species are markedly different and that the expansion into North‐West Africa by J. deserti was more recent than that of J. jaculus. The weak ecological separation between species and the signs of recent population growth and expansion of J. deserti suggest that its sympatric occurrence with J. jaculus is recent and that these species evolved in isolated populations, after diverging around the Pliocene–Pleistocene boundary. The importance of climate changes on the Sahara Desert biota is discussed in the context of genetic diversification. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 435–445.     

New perspectives on the origin and diversification of Africa's forest avifauna

The use of DNA sequence data in systematic studies has brought about a revolution in our understanding of avian relationships and when combined with digitized distributional data, has facilitated new interpretations about the origins of diverse clades of the African avifauna including its diversification up through the Tertiary until the present. Here we review recent studies with special reference to Africa's forest avifauna and specifically comment on the putative origins of 'hotspots' of endemism in the Eastern Arc Mountains of Tanzania and in the Cape Region of South Africa. Intriguingly, both these areas appear to have retained populations of relict taxa since the mid-tertiary thermal optimum and at the same time have been centres of recent species differentiation.     

Early survival and growth of Allanblackia stuhlmannii (Clusiaceae): a threatened tropical rainforest tree of high economic value in Tanzania

Rural households living in tropical ecosystems depend heavily on forest trees for valuable nontimber forest products that are, however, undergoing unsustainable harvesting. This study assessed early survival and growth of Allanblackia stuhlmannii (Clusiaceae), a nontimber tree species endemic to Tanzania. A total of 400 seedlings sourced from twenty elite female trees were planted in two adjacent locations. Data were collected over 59 months for survival, height and root collar diameter. Seedling survival at 59 months was significantly different between Emau and Shebomeza, being on average ~11% higher in Shebomeza. However, survival of the progenies of each female tree at 59 months was not significantly different. Overall, mean RCD (range: 6.8–59.7 mm) and height (range: 17.1–274.4 cm) were positively correlated (r = 0.84, P < 0.001). The correlations in heights of individuals between 17 and 59, and 23 and 59 months were positive (r = 0.34 versus 0.53, respectively). Results also suggested that if growth rate is related to ontogeny from juvenile to adult, then the progenies of ten female trees that have shown consistently higher growth rates may flower and fruit earlier than other progenies. Future planting for conservation of this threatened, overharvested tree species can therefore be based on data gathered from these field genebanks.     

High species diversity in one of the dominant groups of spiders in East African montane forests (Araneae: Pholcidae: Buitinga n. gen., Spermophora Hentz)

The six-eyed pholcid spiders of East Africa are revised. A new genus is recognized, Buitinga n. gen ., with 17 new species and three species transferred from Spermophora Hentz. The new genus is characterized by the presence of a scape on the epigynum. This scape may be straight or tightly curled up at rest, and is usually highly expandable. Seven additional African and Comoran species are newly described and tentatively assigned to Spermophora . A data matrix with 60 characters and 77 taxa (including 20 East African species and 25 additional Spermophora and ' Spermophora -like' species) is analysed cladistically. Buitinga is closer to the genera Paramicromerys Millot (endemic in Madagascar) and Spermophorides Wunderlich (Mediterranean and Canary Islands) as well as to several African and Comoran species tentatively assigned to Spermophora than to the type species of Spermophora . It is argued that current estimates of species numbers may be inaccurate and that pholcids may turn out to be one of the most diverse spider families.  © 2003 The Linnean Society of London. Zoological Journal of the Linnean Society, 2003, 137, 555−619     

PERMANENT GENETIC RESOURCES: Isolation and characterization of 10 tetranucleotide microsatellite loci in an enigmatic East African bird, the spot-throat (Modulatrix stictigula)

We describe the isolation of 10 tetranucleotide microsatellites from the spot-throat using an enrichment protocol. All loci were highly variable with the number of alleles ranging from six to 20 and observed heterozygosity ranging from 0.410 to 0.940. Although all loci were in Hardy-Weinberg equilibrium, locus Mst95 showed significant homozygote excess in both surveyed populations, possibly a consequence of the presence of null alleles at this locus. These loci will be used to determine the extent to which spot-throat populations are isolated in order to help set conservation priorities for this ancient African lineage.     

Effects of forest disturbance on the fitness of an endemic rodent in a biodiversity hotspot

Praomys delectorum occurs abundantly in both disturbed and intact forests in the Ukaguru Mountains within the Eastern Arc Mountains (EAM), Morogoro, Tanzania. While previous studies have reported that anthropogenic disturbances such as grazing, wood cutting, and harvesting have a positive effect on the population density of P. delectorum, the impact of habitat disturbance on its demographic traits is still unknown. We performed a capture–mark–recapture study in both disturbed and intact forests from June 2018 to February 2020 in order to investigate the effects of habitat disturbance on abundance and two demographic traits: survival and maturation of P. delectorum in the Ukaguru Mountains. We found no variation in abundance or maturation between intact and disturbed forests, but habitat type did affect survival. However, this effect was sex‐dependent since female survival was higher in disturbed forests, while male survival remained similar across the two forest types potentially due to differences in predation pressure or food availability between the two habitats. Continuous demographic monitoring of P. delectorum in EAM is necessary given that the increasing human population surrounding the landscape is leading to higher deforestation rates and expansion of the pine plantation in the forest reserve.     

Patterns of molecular evolution and diversification in a biodiversity hotspot: the California Floristic Province

The California Floristic Province harbours more endemic plant and animal taxa and more identifiable subspecies than any other area of comparable size in North America. We present evidence that physical historical processes have resulted in congruent patterns of genetic diversity over the past 2-10 million years. Using a molecular clock approach we show that diversification and establishment of spatial genetic structure across six taxonomic groups coincide with the putative age of California's mountain ranges and aridification in the region. Our results demonstrate the importance of geographical barriers and climatological events to species diversification and the overall geographical structure of biodiversity. These results should facilitate conservation efforts in this biodiversity hotspot for taxa whose population genetic structure is still unknown and may suggest the potential utility of this approach in regional conservation planning efforts.     

Mosaics in the mangroves: allopatric diversification of tree‐climbing mudwhelks (Gastropoda: Potamididae: Cerithidea) in the Indo‐West Pacific

The Indo‐Australian Archipelago (IAA) is the richest area of biodiversity in the marine realm, yet the processes that generate and maintain this diversity are poorly understood and have hardly been studied in the mangrove biotope. Cerithidea is a genus of marine and brackish‐water snails restricted to mangrove habitats in the Indo‐West Pacific, and its species are believed to have a short pelagic larval life. Using molecular and morphological techniques, we demonstrate the existence of 15 species, reconstruct their phylogeny and plot their geographical ranges. Sister species show a pattern of narrowly allopatric ranges across the IAA, with overlap only between clades that show evidence of ecological differentiation. These allopatric mosaic distributions suggest that speciation may have been driven by isolation during low sea‐level stands, during episodes preceding the Plio‐Pleistocene glaciations. The Makassar Strait forms a biogeographical barrier hindering eastward dispersal, corresponding to part of Wallace's Line in the terrestrial realm. Areas of maximum diversity of mangrove plants and their associated molluscs do not coincide closely. © 2013 The Natural History Museum. Biological Journal of the Linnean Society © 2013 The Linnean Society of London, 2013, 110 , 564–580.     

Molecular evidence for the hybrid origin of a new endemic species of Stylosanthes Sw. (Fabaceae) from the Mexican Yucatán Peninsula

Stylosanthes aff. calcicola is a formally undescribed tetraploid species from the Mexican Yucatán Peninsula, showing morphological similarities to the diploid species S. calcicola , but distinct in a number of characters. We used uni- and biparentally inherited molecular markers to infer the hybrid origin of this species in relation to known diploid species of Stylosanthes . Molecular characterization was based on length and/or DNA sequence variation of nuclear sequence-tagged site (STS) markers, the internal transcribed spacer (ITS) region of nuclear rDNA and the trnL intron of chloroplast DNA (cpDNA). Stylosanthes aff. calcicola contains a distinct cpDNA haplotype and nuclear DNA fragment, with closest relationship to the diploid species S. calcicola . In contrast, the DNA sequences of two nuclear loci reveal a closer relationship to the diploid species S. angustifolia , S. hispida , S. humilis , S. leiocarpa and S. viscosa . The majority of the STS markers showed additivity of PCR fragments in S. aff. calcicola , representing the combination of two genetically different genomes. We postulate that S. aff. calcicola is a distinct species of allotetraploid origin that appears to have originated once from hybridization between two divergent genomes, of which the maternal and paternal parent are closely related to, or derived from, a member of the lineages represented by S. calcicola and S. viscosa , respectively.  © 2002 The Linnean Society of London, Botanical Journal of the Linnean Society , 140 , 1–13.     

Historical biogeography and diversification within the Neotropical parrot genus Pionopsitta (Aves: Psittacidae)

Aim We investigate spatial and temporal patterns of diversification within the Neotropical avifauna using the phylogenetic history of parrots traditionally belonging to the genus Pionopsitta Bonaparte 1854. This genus has long been of interest for those studying Neotropical biogeography and diversity, as it encompasses species that occur in most Neotropical forest areas of endemism. Location The Neotropical lowland forests in South and Central America. Methods Phylogenetic relationships were investigated for all species of the genus Pionopsitta and five other short‐tailed parrot genera using complete sequences of the mitochondrial genes cyt b and ND2 as well as 26 plumage characters. The resulting phylogeny was used to test the monophyly of the genus, investigate species limits, and as a framework for reconstructing their historical biogeography and patterns of diversification. Results We found that the genus Pionopsitta, as previously defined, is not monophyletic and thus the Chocó, Central American and Amazonian species will now have to be placed in the genus Gypopsitta. The molecular and morphological phylogenies are largely congruent, but disagree on the position of one of the Amazon basin taxa. Using molecular sequence data, we estimate that species within Gypopsitta diversified between 8.7 and 0.6 Ma, with the main divergences occurring between 3.3 and 6.4 Ma. These temporal results are compared to other taxa showing similar vicariance patterns. Main conclusions The results suggest that diversification in Gypopsitta was influenced mainly by geotectonic events, marine transgressions and river dynamics, whereas Quaternary glacial cycles of forest change seem to have played a minor role in the origination of the currently recognized species.     

Ogasawaracris gloriosus, a new genus and species of possibly extinct grasshopper (Orthoptera: Acrididae) from the Ogasawara Islands

A new grasshopper genus and species of the subfamily Eyprepocnemidinae, Ogasawaracris gloriosus, is described from the Ogasawara Islands, oceanic islands south of Japan. This species has unique characteristics, such as an extraordinarily large body, rugose and very coarse punctation on the lateral surface of the pronotum, and very strong pronotal lateral carinae. Specimens of this new species have rarely been collected and they are known only from the Ogasawara Islands. The species may already be extinct.