The bii4africa dataset of faunal and floral population intactness estimates across Africa's major land uses

Sub-Saharan Africa is under-represented in global biodiversity datasets, particularly regarding the impact of land use on species' population abundances. Drawing on recent advances in expert elicitation to ensure data consistency, 200 experts were convened using a modified-Delphi process to estimate 'intactness scores': the remaining proportion of an 'intact' reference population of a species group in a particular land use, on a scale from 0 (no remaining individuals) to 1 (same abundance as the reference) and, in rare cases, to 2 (populations that thrive in human-modified landscapes). The resulting bii4africa dataset contains intactness scores representing terrestrial vertebrates (tetrapods: ±5,400 amphibians, reptiles, birds, mammals) and vascular plants (±45,000 forbs, graminoids, trees, shrubs) in sub-Saharan Africa across the region's major land uses (urban, cropland, rangeland, plantation, protected, etc.) and intensities (e.g., large-scale vs smallholder cropland). This dataset was co-produced as part of the Biodiversity Intactness Index for Africa Project. Additional uses include assessing ecosystem condition; rectifying geographic/taxonomic biases in global biodiversity indicators and maps; and informing the Red List of Ecosystems.

The status of Tomopterna pulchra Boulenger, 1896 (Anura: Pyxicephalidae)

Tomopterna pulchra (Boulenger, 1896) was described from Lake Tanganyika based on a single specimen. It was synonymised with Tomopterna tuberculosa (Boulenger, 1882) by Loveridge (1957) who noted that it did not fully agree with the description of T. tuberculosa, especially in the difference in dorsal colouration. Genetic differences show that two species are confused, although their advertisement calls and morphology are similar, except for the presence of a pale vertebral stripe mostly in eastern populations. We consider the advertisement calls, morphology, and genetic differences, and remove Tomopterna pulchra (Boulenger, 1896) from the synonymy of Tomopterna tuberculosa. Divergence dating shows that these two species separated in the mid-Miocene. Tomopterna pulchra breeds in rocky habitats, whereas T. tuberculosa breeds in sandy areas, typical of the genus. Based on genetically confirmed specimens, presently T. tuberculosa is known in the west (Angola and Namibia) while T. pulchra is only known from the east (Zambia and Tanzania). The examination of specimens for the presence or absence of a vertebral stripe infers that these species are widespread. Further work is required to determine if the two species are sympatric, and the extent of their ranges.

Chromosomes in the African Frog Genus Tomopterna (Pyxicephalidae) and Probing the Origin of Tetraploid Tomopterna tandyi. Genome 2022;65:585-604. [PMID: 36223652 DOI: 10.1139/gen-2022-0053]

Speciation by polyploidization has been documented to have independently occurred in 12 families of anuran amphibians. Tomopterna tandyi was described as a South African allotetraploid species of sand frogs in the family Pyxicephalidae. Recent taxonomic revisions and new species descriptions in the genus present problems with respect to the evolution of this tetraploid species. Chromosomes, mitochondrial and nuclear gene sequences, isozymes, and male mating calls were examined for T. tandyi and for diploid species of Tomopterna. Mitochondrial sequences confirmed the diploid species, T. adiastola, to be the maternal ancestor that gave rise to the tetraploid about 5 MYA. Nuclear sequences and isozymes reveal a complex reticulation of paternal ancestry that may be explained by occasional hybridization of T. tandyi with diploid species of Tompoterna at various times in sympatric populations. Interspecific diploid to tetraploid gene introgression is suspected to have also occurred in Australian and North American tetraploid species of frogs. Diploid to tetraploid introgression is facilitated through triploid hybrids that are more viable than diploid hybrids and produce unreduced triploid eggs.

The role of cultural norms in shaping attitudes towards amphibians in Cape Town, South Africa

Urban ecosystems are increasingly viewed as an important component within strategies for wildlife conservation but are shaped as much by natural systems as they are by social and political processes. At the garden scale, attitudes and preferences govern design and maintenance choices including the decision to encourage or discourage specific faunal presence. At the global scale, charismatic taxa that are well-liked attract more conservation funding and volunteer stewardship. Amphibians are a class of animals that are both loved and loathed making them a suitable subject for comparing and unpacking the drivers of preference and attitudes towards animals. We conducted a mixed methods survey of 192 participants in three adjacent neighbourhoods in Cape Town, South Africa. The survey included both quantitative and qualitative questions which were analysed thematically and used to explain the quantitative results. The results revealed that attitudes formed during childhood tended to be retained into adulthood, were shaped by cultural norms, childhood experiences and the attitudes of primary care-givers. The findings are significant for environmental education programmes aimed at building connectedness to nature and biophilic values.

Sexual Dichromatism Drives Diversification within a Major Radiation of African Amphibians

Theory predicts that sexually dimorphic traits under strong sexual selection, particularly those involved with intersexual signaling, can accelerate speciation and produce bursts of diversification. Sexual dichromatism (sexual dimorphism in color) is widely used as a proxy for sexual selection and is associated with rapid diversification in several animal groups, yet studies using phylogenetic comparative methods to explicitly test for an association between sexual dichromatism and diversification have produced conflicting results. Sexual dichromatism is rare in frogs, but it is both striking and prevalent in African reed frogs, a major component of the diverse frog radiation termed Afrobatrachia. In contrast to most other vertebrates, reed frogs display female-biased dichromatism in which females undergo color transformation, often resulting in more ornate coloration in females than in males. We produce a robust phylogeny of Afrobatrachia to investigate the evolutionary origins of sexual dichromatism in this radiation and examine whether the presence of dichromatism is associated with increased rates of net diversification. We find that sexual dichromatism evolved once within hyperoliids and was followed by numerous independent reversals to monochromatism. We detect significant diversification rate heterogeneity in Afrobatrachia and find that sexually dichromatic lineages have double the average net diversification rate of monochromatic lineages. By conducting trait simulations on our empirical phylogeny, we demonstrate that our inference of trait-dependent diversification is robust. Although sexual dichromatism in hyperoliid frogs is linked to their rapid diversification and supports macroevolutionary predictions of speciation by sexual selection, the function of dichromatism in reed frogs remains unclear. We propose that reed frogs are a compelling system for studying the roles of natural and sexual selection on the evolution of sexual dichromatism across micro- and macroevolutionary timescales.

Correction to the type locality of Tomopterna ahli (Deckert, 1938) (Anura: Pyxicephalidae), with the designation of a neotype

Deckert described a Tomopterna as Arthroleptella ahli from South Africa in 1938. We demonstrate that the type of Tomopterna ahli (Deckert, 1938) was actually collected in Namibia, and that this nomen is a senior synonym of Tomopterna damarensis Dawood Channing, 2002. We designate a neotype for Tomopterna ahli (Deckert, 1938).

A new grass frog with rupicolous tadpoles from northern Zambia (Anura: Ptychadenidae)

We describe a new species of Ptychadena from Mutinondo Wilderness in northern Zambia. It has rupicolous tadpoles that develop in a film of water. The species is distinguished on morphology, advertisement call and DNA sequences from other grass frogs and was found to be most closely related to P. broadleyi. It has no contrasting longitudinal bands on the posterior thigh, the foot is longer than half SVL, it has no light triangle on the snout, three phalanges of the fourth toe free of web and the snout has no skin folds. The species should be considered Near Threatened in terms of the IUCN Red List criteria given its limited extent of occurrence and population size.

A review of active hot-spring analogues of Rhynie: environments, habitats and ecosystems

The Lower Devonian Rhynie chert formed as silica sinter entombed an early terrestrial ecosystem. Silica sinter precipitates only from water flowing from alkali-chloride hot springs and geysers, the surface expression of crustal-scale geothermal systems that form low-sulfidation mineral deposits in the shallow subsurface. Active alkali-chloride hot springs at Yellowstone National Park create a suite of geothermally influenced environments; vent pools, sinter aprons, run-off streams, supra-apron terrace pools and geothermal wetlands that are habitats for modern hot-spring ecosystems. The plant-rich chert, which makes Rhynie internationally famous, probably formed in low-temperature environments at the margins of a sinter apron where frequent flooding by geothermal water and less frequent flooding by river waters created ephemeral to permanent wetland conditions. Here, the plants and associated microbes and animals would be immersed in waters with elevated temperature, brackish salinity, high pH and a cocktail of phytotoxic elements which created stresses that the fossil ecosystem must have tolerated. The environment excluded coeval mesophytic plants, creating a low-diversity hot-spring flora. Comparison with Yellowstone suggests the Rhynie plants were preadapted to their environment by life in more common and widespread environments with elevated salinity and pH such as coastal marshes, salt lakes, estuaries and saline seeps.This article is part of a discussion meeting issue 'The Rhynie cherts: our earliest terrestrial ecosystem revisited'.

Leapfrogging into new territory: How Mascarene ridged frogs diversified across Africa and Madagascar to maintain their ecological niche

The Mascarene ridged frog, Ptychadena mascareniensis, is a species complex that includes numerous lineages occurring mostly in humid savannas and open forests of mainland Africa, Madagascar, the Seychelles, and the Mascarene Islands. Sampling across this broad distribution presents an opportunity to examine the genetic differentiation within this complex and to investigate how the evolution of bioclimatic niches may have shaped current biogeographic patterns. Using model-based phylogenetic methods and molecular-clock dating, we constructed a time-calibrated molecular phylogenetic hypothesis for the group based on mitochondrial 16S rRNA and cytochrome b (cytb) genes and the nuclear RAG1 gene from 173 individuals. Haplotype networks were reconstructed and species boundaries were investigated using three species-delimitation approaches: Bayesian generalized mixed Yule-coalescent model (bGMYC), the Poisson Tree Process model (PTP) and a cluster algorithm (SpeciesIdentifier). Estimates of similarity in bioclimatic niche were calculated from species-distribution models (maxent) and multivariate statistics (Principal Component Analysis, Discriminant Function Analysis). Ancestral-area reconstructions were performed on the phylogeny using probabilistic approaches implemented in BioGeoBEARS. We detected high levels of genetic differentiation yielding ten distinct lineages or operational taxonomic units, and Central Africa was found to be a diversity hotspot for these frogs. Most speciation events took place throughout the Miocene, including "out-of-Africa" overseas dispersal events to Madagascar in the East and to São Tomé in the West. Bioclimatic niche was remarkably well conserved, with most species tolerating similar temperature and rainfall conditions common to the Central African region. The P. mascareniensis complex provides insights into how bioclimatic niche shaped the current biogeographic patterns with niche conservatism being exhibited by the Central African radiation and niche divergence shaping populations in West Africa and Madagascar. Central Africa, including the Albertine Rift region, has been an important center of diversification for this species complex.

The phylogenetic position and diversity of the enigmatic mongrel frog Nothophryne Poynton, 1963 (Amphibia, Anura)

The phylogenetic relationships of the African mongrel frog genus Nothophryne are poorly understood. We provide the first molecular assessment of the phylogenetic position of, and diversity within, this monotypic genus from across its range-the Afromontane regions of Malawi and Mozambique. Our analysis using a two-tiered phylogenetic approach allowed us to place the genus in Pyxicephalidae. Within the family, Nothophryne grouped with Tomopterna, a hypothesis judged significantly better than alternative hypotheses proposed based on morphology. Our analyses of populations across the range of Nothophryne suggest the presence of several cryptic species, at least one species per mountain. Formal recognition of these species is pending but there is a major conservation concern for these narrowly distributed populations in an area impacted by major habitat change. The phylogenetic tree of pyxicephalids is used to examine evolution of life history, ancestral habitat, and biogeography of this group.

Taxonomy of the super-cryptic Hyperolius nasutus group of long reed frogs of Africa (Anura: Hyperoliidae), with descriptions of six new species

Specimens from across the range of the Hyperolius nasutus species group were sequenced for two mitochondrial genes and one nuclear gene. Advertisement calls were recorded from the same specimens where possible, and morphological characters were compared. Bayesian inference and maximum likelihood produced a tree indicating 16 clades. The clades show little or no overlap in combinations of 16S sequence difference, shared tyr haplotypes, advertisement call parameters, snout profiles and webbing. On the basis of these data we recognise H. acuticeps, H. adspersus, H. benguellensis, H. dartevellei, H. igbettensis, H. nasutus, H. nasicus, H. poweri, H. viridis and describe six new species: Hyperolius friedemanni sp. nov. Mercurio & Rödel, Hyperolius howelli sp. nov. Du Preez & Channing, Hyperolius inyangae sp. nov. Channing, Hyperolious jacobseni sp. nov. Channing, Hyperolius rwandae sp. nov. Dehling, Sinsch, R6del & Channing, and Hyperolius lupiroensis sp. nov. Channing. Hyperolius lamottei is confirmed to be outside the H. nasutus group clade. Hyperolius granulatus, H. oxyrhynchus, H. punctulatus and H. sagitta are assigned as junior synonyms. As our results are based on a small number of specimens, these hypotheses await testing with larger sample sizes and more characters. A species distribution model suggests where outlier populations might be found.

Maternal hyperoxygenation improves left heart filling in fetuses with atrial septal aneurysm causing impediment to left ventricular inflow

OBJECTIVES

Aneurysm of the atrial septum (AAS) with excessive excursion of septum primum into the left atrium is an uncommon and relatively benign fetal condition associated with impediment to left ventricular (LV) filling and the appearance of a slender, but apex-forming, LV on fetal echocardiography. Impediment to filling can be severe, creating the image of LV hypoplasia with retrograde aortic flow. We hypothesize that maternal hyperoxygenation alters atrial septal position, improves LV filling, and normalizes aortic flow in fetuses with AAS by increasing fetal pulmonary venous return.

METHODS

Fetal echocardiography was performed prior to, and at 10 min of, maternal hyperoxygenation in 12 fetuses with AAS who were referred to our center because of LV hypoplasia. Atrial septal excursion (ASE), LV and right ventricular (RV) sphericity index (SI) and direction of flow in the aortic isthmus, as determined by Doppler, were measured.

RESULTS

With maternal hyperoxygenation, mean ± SD ASE decreased (0.76 ± 0.17 before maternal hyperoxygenation vs 0.53 ± 0.23 after maternal hyperoxygenation; P < 0.01), consistent with increased pulmonary venous return, LV-SI increased (0.29 ± 0.06 vs 0.42 ± 0.06; P < 0.001), indicating increased LV filling, and the direction of aortic isthmus flow changed from retrograde in all cases prior to maternal hyperoxygenation to antegrade in 10 and to bidirectional in two. RV-SI remained unchanged (0.53 ± 0.13 vs 0.52 ± 0.10; P = 0.7).

CONCLUSIONS

In cases of AAS, short-term maternal hyperoxygenation increases fetal pulmonary venous return, substantially alters LV geometry and promotes antegrade flow in the aortic isthmus. This demonstrates proof-of-concept that maternal hyperoxygenation can improve filling of the left side of the fetal heart in AAS.

The Maluti Mystery revisited: Taxonomy of African River Frogs (Pyxicephalidae, Amietia) on the Drakensberg Mountains in southern Africa

The taxonomy of two similar frogs from the top of the Drakensberg escarpment, the Maluti River Frog and the Phofung River Frog is not settled. I examine the relevant types and type descriptions, and discover a number of errors in the literature. Some of the recent taxonomic changes were found to be unsupported. The Maluti River Frog is assigned to Amietia vertebralis (Hewitt, 1927), and the Phofung River Frog to Amietia hymenopus (Boulenger, 1920).

Identification of sand frogs (Anura: Pyxicephalidae: Tomopterna) from Kenya with the description of two new species

African sand frogs in the genus Tomopterna presently include 13 species. These are known to be highly cryptic and morphologically similar. Despite increased effort in the recent past, the taxonomy of the group is still unresolved and some populations e.g. in Kenya have remained largely unstudied. This paper starts to address this gap using molecular, advertisement call and morphological comparisons. We test the boundaries of the Kenyan species based on mitochondrial 16S rRNA sequence data. Two new species are recognised and described: Tomopterna wambensis sp. nov. and Tomopterna gallmanni sp. nov. Further molecular and advertisement call studies of Tomopterna populations in Kenya are recommended, especially for those populations previously identified as T. cryptotis and T. tandyi.

Amietia angolensis and A. fuscigula (Anura: Pyxicephalidae) in southern Africa: a cold case reheated

A study combining DNA sequences of the mitochondrial 16S rRNA gene, advertisement calls and morphology of some southern African river frogs confirms Amietia vandijki (Visser & Channing, 1997) as a good species. The form presently referred to as Amietia angolensis in southern Africa is shown to comprise two species: Amietia angolensis (Bocage, 1866) known from Angola, and Amietia quecketti (Boulenger, 1895) known from South Africa, Zimbabwe and Lesotho. Junior synonyms of A. quecketti include Rana theileri Mocquard, 1906 and Afrana dracomontana Channing, 1978. The form presently known as Amietia fuscigula is shown to consist of two distantly related taxa: Amietia fuscigula (Duméril & Bibron, 1841) from the south-western Cape and an undescribed species that we here name Amietia poyntoni sp. nov. Channing & Baptista, known from the rest of South Africa and Namibia. These five species have large differences in 16S sequences, as well as differences in morphology and advertisement call. Call and molecular data are both diagnostic, while morphology shows some overlap between taxa. An extended study of the genus across Africa is in preparation.

Equisetum thermale sp. nov. (Equisetales) from the Jurassic San Agustín hot spring deposit, Patagonia: anatomy, paleoecology, and inferred paleoecophysiology

PREMISE OF THE STUDY

Dated molecular phylogenies suggest a Cenozoic origin for the crown group of Equisetum. but compression fossil equisetaleans that are morphologically indistinguishable from extant Equisetum and recently discovered anatomically preserved examples strongly suggest an earlier Mesozoic initial diversification.

METHODS

In situ samples of Equisetum thermale sp. nov. from the Upper Jurassic San Agustín hot spring deposit were collected and studied with the use of polished blocks, thin sections, and light microscopy.

KEY RESULTS

Equisetum thermale exhibits all the morphological and anatomical characteristics of the extant crown group Equisetum. It shows a mixture of features present in the two extant subgenera, e.g., superficial stomata typical of subgenus Equisetum allied with infrequently ramifying stems typical of subgenus Hippochaete. This appears to ally E. thermale with the least derived extant species in the genus Equisetum bogotense (sister species to the two subgenera). Its association of hydromorphic and xeromorphic characters allowed it to grow as an emergent aquatic in physically and chemically stressed geothermally influenced wetlands, where it formed dense monospecific stands. Equisetum thermale, because it is preserved in situ with intact anatomy, provides clear paleoecological, biological, plus inferred paleoecophysiological evidence of adaptations known in extant species.

CONCLUSIONS

As the earliest unequivocal member of the genus, E. thermale supports the hypothesis of a Mesozoic origin. Its inferred tolerance of a similar range of stresses (e.g., high salinity, alkalinity, and heavy metal concentrations) to that seen in extant Equisetum suggests early evolution and subsequent maintenance of ecophysiological innovations in the genus.

The impact of conservation on the status of the world's vertebrates

Using data for 25,780 species categorized on the International Union for Conservation of Nature Red List, we present an assessment of the status of the world's vertebrates. One-fifth of species are classified as Threatened, and we show that this figure is increasing: On average, 52 species of mammals, birds, and amphibians move one category closer to extinction each year. However, this overall pattern conceals the impact of conservation successes, and we show that the rate of deterioration would have been at least one-fifth again as much in the absence of these. Nonetheless, current conservation efforts remain insufficient to offset the main drivers of biodiversity loss in these groups: agricultural expansion, logging, overexploitation, and invasive alien species.

Achieving operational efficiencies using a DRG-based tracer approach

Hospitals can use a DRG-based tracer approach to analyze and correct inefficiencies in the flow of care delivery. The approach works best when the analysis is focused on a high-volume DRG. In the case of Mount Sinai Hospital in Chicago, this approach was instrumental in improving efficiencies of care processes associated with DRG 143: chest pain.

The value of value-based purchasing

In the first four years of the Hospital Quality Incentive Demonstration (HQID) project operated by the Centers for Medicare & Medicaid Improvement (CMS) and Premier, Inc., HQID hospitals improved their composite quality scores by 17.2 percent across five clinical areas. If every hospital were able to replicate this level of performance, an estimated $4.5 billion and 70,000 lives would be saved each year, according to CMS and Premier.

Nuclear gene phylogeny of narrow-mouthed toads (Family: Microhylidae) and a discussion of competing hypotheses concerning their biogeographical origins

The family Microhylidae has a large circumtropic distribution and contains about 400 species in a highly subdivided taxonomy. Relationships among its constituent taxa remained controversial due to homoplasy in morphological characters, resulting in conflicting phylogenetic hypotheses. A phylogeny based on four nuclear genes (rag-1, rag-2, tyrosinase, BDNF) and one mitochondrial gene (CO1) of representatives of all currently recognized subfamilies uncovers a basal polytomy between several subfamilial clades. A sister group relationship between the cophylines and scaphiophrynines is resolved with moderate support, which unites these endemic Malagasy taxa for the first time. The American members of the subfamily Microhylinae are resolved to form a clade entirely separate from the Asian members of that subfamily. Otophryne is excluded from the subfamily Microhylinae, and resolved as a basal taxon. The placement of the Asian dyscophine Calluella nested within the Asian Microhyline clade rather than with the genus Dyscophus is corroborated by our data. Bayesian estimates of the divergence time of extant Microhylidae (47-90 Mya) and among the subclades within the family are discussed in frameworks of alternative possible biogeographic scenarios.