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SummaryDocumenting phylogenetic diversity for conservation practice allows elucidation of ecosystem functioning and processes by highlighting the commonality and divergence of species’ functional traits within their evolutionary context. Conserving distinct evolutionary histories has intrinsic value, and the conservation of phylogenetically diverse communities is more likely to preserve distinct or relic evolutionary lineages. We explored the potential for anthropogenic forest fragmentation to act as a selective filter of avian phylogenetic diversity within the community of forest-dependent birds of the critically endangered Indian Ocean Coastal Belt Forest (IOCBF), South Africa. We conducted avian point count surveys during the austral breeding season, and calculated fragmentation metrics of forest structural complexity, patch size and isolation. We constructed a maximum likelihood phylogeny using the combined analysis of two mitochondrial genes and three nuclear markers and measured the influence of the fragmentation metrics on six measures of phylogenetic diversity. Our results indicated that the avian community was variously affected by anthropogenic forest fragmentation, with the different metrics of phylogenetic diversity responding with no definitive overall pattern. However, forest structural complexity emerged as an important metric explaining phylogenetic structuring. While the avian community’s phylogenetic diversity displayed resilience to anthropogenic fragmentation, previous research showed a reduction in functional diversity along the fragmentation gradient. Therefore, we recommend studies that especially aim to guide conservation management, incorporate both phylogenetic and functional diversity measures to sufficiently interrogate communities’ resilience to the threats under investigation.

Zooplankton plays an essential role in marine ecosystems as the link between primary producers (phytoplankton) and higher trophic levels in food webs, and as a dynamic pool of recruits for invertebrates and fish. Zooplankton communities are diverse with a patchy distribution at different spatial scales, influenced by oceanographic processes. The continental shelf of eastern South Africa is narrow and exposed to the western-boundary Agulhas Current, with some shelter against strong directional flow provided by the broader KwaZulu-Natal Bight, a coastal offset adjacent to an estuary. We compared zooplankton species richness, diversity and relative abundance of key taxa among sheltered and exposed shelf areas using metabarcoding and community analysis, to explore the ecological role of the bight in a highly dynamic ocean region. Metabarcoding recovered higher richness and diversity at a finer resolution than could previously be achieved with traditional microscopy. Of 271 operational taxonomic units (OTUs) recovered through metabarcoding, 63% could be matched with95% sequence similarity to reference barcodes. OTUs were dominated by malacostracan crustaceans (161 spp.), ray-finned fishes (45 spp.) and copepods (28 spp.). Species richness, diversity and the relative abundance of key taxa differed between sheltered and exposed shelf areas. Lower species richness in the bight was partly attributed to structurally homogeneous benthic habitats, and an associated reduction of meroplanktonic species originating from local benthic-pelagic exchange. High relative abundance of a ray-finned fish in the bight, as observed based on fish eggs and read counts, confirmed that the bight is an important fish spawning area. Overall, zooplankton metabarcoding outputs were congruent with findings of previous ecological research using more traditional methods of observation.

Metabarcoding is an emerging method in which DNA barcoding is combined with next-generation sequencing to determine the biodiversity of taxonomically complex samples. We assessed the current state of DNA barcode reference databases for marine zooplankton in South Africa and undertook a metabarcoding analysis to determine the species composition of samples collected with plankton tow nets. Analysis of DNA sequences mined from the literature and in online barcode reference databases revealed incomplete records for all taxa examined. Barcode records were dominated by meroplanktonic species with commercially important life-history phases (fishes and decapod crustaceans) and by species occurring in easily accessible nearshore habitats. Holoplanktonic species were underrepresented, despite making up the bulk of zooplankton biodiversity, including most potential indicator species. Metabarcoding analysis of plankton samples could identify 45% of amplicon sequence variants to species level based on BOLD databases (123 species) and similar numbers using GenBank and the MIDORI COI classifier. Morphological analysis of samples could not achieve comparable resolution at species level, but with some exceptions it recovered similar classes of organisms to those found by metabarcoding. The need for integrative molecular/morphological studies to increase and validate barcode reference databases of key zooplankton taxa is recognised. Metabarcoding of marine zooplankton in South Africa has now been successfully undertaken and the methodology is expected to facilitate high-resolution monitoring of zooplankton biodiversity in pelagic ecosystems and accelerate the discovery of new species.

Background The bearded vulture is sparsely distributed across a wide geographic range that extends over three continents (Africa, Europe and Asia). Restriction to high-altitude mountainous habitats, low breeding rates, lack of food and a heightened level of persecution have left many local populations severely diminished or extinct. Understanding the genetic connectivity and population structure of this threatened vulture species is critical for accurately assessing their conservation status, and for appropriately managing local populations through captive breeding programmes or translocations. Previous genetic assessments of the species were mainly focused on the European and Asian populations and included limited representation of the geographically isolated southern African population. A single mitochondrial study, which focused on the African populations of the bearded vulture, detected limited genetic differentiation between populations in Ethiopia and southern Africa, with reduced haplotype diversity in the southern Africa population. In this study, we extend the previous genetic assessments of the species by examining the phylogeography and genetic connectivity of global G. barbatus populations using a panel of 14 microsatellite loci. Results Analyses revealed spatially correlated genetic differentiation between regional populations and low levels of gene flow between these population fragments. In contrast to the mitochondrial data, the microsatellite data support the management of genetically different populations as separate entities. Conclusions Low genetic diversity and geographic isolation are known to adversely affect the evolutionary potential of a species in the long-term. The high inbreeding found in the southern African G. barbatus and, to a lesser extent, the northern African populations highlights the need for conservation programmes to effectively manage populations of this species and maintain extant genetic diversity.

Aim We incorporated genetic structure and life history phase in species distribution models (SDMs) constructed for a widespread spiny lobster, to reveal local adaptations specific to individual subspecies and predict future range shifts under the RCP 8.5 climate change scenario. Location Indo‐West Pacific. Methods MaxEnt was used to construct present‐day SDMs for the spiny lobster Panulirus homarus and individually for the three genetically distinct subspecies of which it comprises. SDMs incorporated both sea surface and benthic (seafloor) climate layers to recreate discrete influences of these habitats during the drifting larval and benthic juvenile and adult life history phases. Principle component analysis (PCA) was used to infer environmental variables to which individual subspecies were adapted. SDM projections of present‐day habitat suitability were compared with predictions for the year 2,100, under the RCP 8.5 climate change scenario. Results In the PCA, salinity best explained P. h. megasculptus habitat suitability, compared with current velocity in P. h. rubellus and sea surface temperature in P. h. homarus. Drifting and benthic life history phases were adapted to different combinations of sea surface and benthic environmental variables considered. Highly suitable habitats for benthic phases were spatially enveloped within more extensive sea surface habitats suitable for drifting larvae. SDMs predicted that present‐day highly suitable habitats for P. homarus will decrease by the year 2,100. Main conclusions Incorporating genetic structure in SDMs showed that individual spiny lobster subspecies had unique adaptations, which could not be resolved in species‐level models. The use of sea surface and benthic climate layers revealed the relative importance of environmental variables during drifting and benthic life history phases. SDMs that included genetic structure and life history were more informative in predictive models of climate change effects., We constructed present‐day species distribution models (SDMs) for the widespread spiny lobster Panulirus homarus and individually for the three genetically distinct subspecies of which it comprises. The SDMs were used to reveal local adaptations specific to individual subspecies and to predict future range shifts under the RCP 8.5 climate change scenario. Our approach included both sea surface and benthic (sea floor) climate layers to recreate discrete influences of these habitats during the drifting larval and benthic adult life history phases. Our analyses confirmed that accounting for genetic partitioning in models of widespread marine species can reveal unique local adaptations, which were unresolved in models that excluded the genetic information.

Populations of wild African Grey parrots (Psittacus erithacus) are declining rapidly driven by the removal of individuals for the pet trade and accelerated habitat destruction and fragmentation. African Greys are currently listed as Endangered on the IUCN Red list and are on Appendix I of CITES, which prohibits all trade in wild-caught individuals. The demand for these parrots in the pet trade can, however, be met through legal trade in captive-bred birds. Determining which birds are captive-bred is often challenging. Genetic techniques have recently become established as a valuable tool in providing accurate information on the paternity of any offspring produced in captivity. Another advantage of using molecular data is that genotypes can also be used for measuring the genetic diversity and degree of relatedness within the captive population to prevent inbreeding. In this study, we test the utility of a suite of previously published microsatellite markers as a molecular tool for parentage analysis. The panel of 11 loci was found to have sufficient discriminatory power to be used in parentage assignment. In this study we present a set of markers that can be used with confidence to determine if a bird has been bred from captive parents and so can be legally traded. These molecular markers were also tested for use on low amounts of DNA extracted from feathers to aid law enforcement authorities to better control legal and illegal trade of this endangered parrot species.

Metabarcoding to determine the species composition and diversity of marine zooplankton communities is a fast-developing field in which the standardization of methods is yet to be fully achieved. The selection of genetic markers and primer choice are particularly important because they substantially influence species detection rates and accuracy. Validation is therefore an important step in the design of metabarcoding protocols. We developed taxon-specific mini-barcode primers for the cytochrome c oxidase subunit I (COI) gene region and used an experimental approach to test species detection rates and primer accuracy of the newly designed primers for prawns, shrimps and crabs and published primers for marine lobsters and fish. Artificially assembled mock communities (with known species ratios) and unsorted coastal tow-net zooplankton samples were sequenced and the detected species were compared with those seeded in mock communities to test detection rates. Taxon-specific primers increased detection rates of target taxa compared with a universal primer set. Primer cocktails (multiple primer sets) significantly increased species detection rates compared with single primer pairs and could detect up to 100% of underrepresented target taxa in mock communities. Taxon-specific primers recovered fewer false-positive or false-negative results than the universal primer. The methods used to design taxon-specific mini-barcodes and the experimental mock community validation protocols shown here can easily be applied to studies on other groups and will allow for a level of standardization among studies undertaken in different ecosystems or geographic locations.

Evolution is driven by natural selection acting on variable phenotypic traits. Understanding the molecular basis of those traits is crucial for elucidating the mechanisms of natural selection. The southern African jackal buzzard (Buteo rufofuscus) displays extreme plumage colour polymorphism, with colouration on the chest varying from dark black to pale white. In a number of birds and other vertebrates, genetic variation at the melanocortin-1 receptor (Mc1r) gene is associated with melanin-based colour variation. Here, the Mc1r gene was sequenced from 12 jackal buzzard individuals displaying three distinct colour morphs (dark, intermediate and pale). A single nucleotide change was found, which although it resulted in an amino acid change, was shared by all jackal buzzards irrespective of colour morph. Although the Mc1r has played an important role in colour polymorphism in other species, in this study no association between Mc1r genotype and plumage polymorphism in jackal buzzards was found.Keywords: Buteo rufofuscus; colouration; melanocortin system; plumage polymorphism

SummaryThe Cape ParrotPoicephalus robustusis a habitat specialist, restricted to forest patches in the Eastern Cape (EC), KwaZulu-Natal (KZN) and Limpopo provinces of South Africa. Recent census estimates suggest that there are less than 1,600 parrots left in the wild, although historical data suggest that the species was once more numerous. Fragmentation of the forest biome is strongly linked to climate change and exploitation of the forest by the timber industry. We examine the subpopulation structure and connectivity between fragmented populations across the distribution of the species. Differences in historical and contemporary genetic structure of Cape Parrots is examined by including both modern samples, collected from 1951 to 2014, and historical samples, collected from 1870 to 1946. A total of 114 individuals (historical = 29; contemporary = 85) were genotyped using 16 microsatellite loci. We tested for evidence of partitioning of genotypes at both a temporal and spatial scales by comparing shifts in allelic frequencies of historical (1870–1946) and contemporary (1951–2014) samples across the distribution of the species. Tests for population bottlenecks were also conducted to determine if anthropogenic causes are the main driver of population decline in this species. Analyses identified three geographically correlated genetic clusters. A southern group restricted to forest patches in the EC, a central group including birds from KZN and a genetically distinct northern Limpopo cluster. Results suggest that Cape Parrots have experienced at least two population bottlenecks. An ancient decline during the mid-Holocene (∼ 1,800-3,000 years before present) linked to climate change, and a more recent bottleneck, associated with logging of forests during the early 1900s. This study highlights the effects of climate change and human activities on an endangered species associated with the naturally fragmented forests of eastern South Africa. These results will aid conservation authorities with the planning and implementation of future conservation initiatives. In particular, this study emphasises the Eastern Cape mistbelt forests as an important source population for the species and calls for stronger conservation of forest patches in South Africa to promote connectivity of forest taxa.

Pollination is a key component in agricultural food production and ecosystem maintenance, with plant–pollinator interactions an important research theme in ecological and evolutionary studies. Natural history collections provide unique access to samples collected at different spatial and temporal scales. Identification of the plant origins of pollen trapped on the bodies of pollinators in these collections provides insight into historic plant communities and pollinators’ preferred floral taxa. In this study, pollen was sampled from Megachile venusta Smith bees from the National Collection of Insects, South Africa, spanning 93 years. Three barcode regions, the internal transcribed spacer 1 and 2 (ITS1 and ITS2) and ribulose‐1,5‐biphosphate carboxylase (rbcL), were sequenced from mixed pollen samples using a next‐generation sequencing approach (MiSeq, Illumina). Sequenced reads were compared to sequence reference databases that were generated by extracting sequence and taxonomic data from GenBank. ITS1 and ITS2 were amplified successfully across all (or most) samples, while rbcL performed inconsistently. Age of sample had no impact on sequencing success. Plant classification was more informative using ITS2 than ITS1 barcode data. This study also highlights the need for comprehensive reference databases as limited local plant sequence representation in reference databases resulted in higher‐level taxon classifications being more confidently interpreted. The results showed that small, insect‐carried pollen samples from historic bee specimens collected from as early as 1914 can be used to obtain pollen metabarcodes. DNA metabarcoding of mixed origin pollen samples provided a faster, more accurate method of determining pollen provenance, without the need for expert palynologists. The use of historic collections to sample pollen directly from pollinators provided additional value to these collections. Sampling pollen from historic collections can potentially provide the spatial and temporal scales for investigations into changes in plant community structure or pollinator floral choice in the face of global climate change.

South Africa is a megadiverse country with three globally recognised biodiversity hotspots within its borders. Bees in particular show high diversity and endemism in the western part of the country. Not much is currently known about the floral host preferences of indigenous bees in South Africa, with data only available from observational studies. Pollen metabarcoding provides provenance information by utilising DNA analyses instead of floral visitation and traditional microscopic identification to identify pollinator food plants, which can be time consuming and imprecise. In this study, we sampled pollen from leaf-cutter bees (Megachilidae) specimens maintained in a historic insect collection (National Collection of Insects, South Africa) that were originally collected from two florally important areas in South Africa (Succulent Karoo and Savanna) and used metabarcoding to determine pollen provenance. We also sampled pollen from leafcutter bee species with wider distributions, that extend across many different biomes, to determine if these ‘generalist’ species show relaxed floral host specificity in some biomes. Metabarcoding involved sequencing of the nuclear internal transcribed spacer 2 (ITS2) region. Amplicons were compared to a sequence reference database to assign taxonomic classifications to family level. Sequence reads were also clustered to OTUs based on 97% sequence similarity to estimate numbers of plant species visited. We found no significant difference in the mean number of plant taxa visited in the Succulent Karoo and Savanna regions, but the widespread group visited significantly more floral hosts. Bees from the widespread group were also characterised by a significantly different composition in pollen assemblage. The time since specimens were collected did not have an effect on the mean number of taxa visited by any of the bee species studied. This study highlights national history collections as valuable sources of temporal and spatial biodiversity data.

Freshwater eels (Anguilla spp.) have a long and complex catadromous life cycle. This unique feature, coupled with difficulty in separating species based on morphology, makes them complex targets for conservation. In this study we evaluated the utility of DNA barcoding using cytochrome oxidase I (COI) to delimit the four species of African eels found in the western Indian Ocean region. We collected 76 individual fin clips from the four eel species (A. mossambica, n=51; A. marmorata, n=17; A. bengalensis, n=6; A. bicolor, n=2) in the rivers of KwaZulu–Natal, South Africa, in 2016–18. Phylogenetic analysis of the COI sequences recovered all four species as monophyletic. Barcoding gap analyses were performed and there was no found overlap in inter- and intraspecific genetic distances. Consequently, the use of COI barcoding as an identification tool was found to be reliable for identifying African eels to the species level, which suggests that this marker should be included in future environmental DNA or metabarcoding studies.

Across the globe, vulture species are experiencing major population declines. A key factor for the long-term persistence of these endangered species is the maintenance of genetic diversity patterns within wild populations. The datasets presented in this descriptor includes microsatellite genotypes of 605 Cape vultures (Gyps coprotheres) drawn from across the southern African distribution of the species. Microsatellites are useful in quantifying genetic diversity at the population level. Populations of the endangered Cape vulture are currently monitored by conservation agencies and the data presented here can be used as an important baseline for future population genetic monitoring., Measurement(s)microsatelliteTechnology Type(s)DNA sequencingFactor Type(s)geographic locationSample Characteristic - OrganismGyps coprotheresSample Characteristic - LocationSouth Africa Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.9896372

The spiny lobster Panulirus homarus rubellus is endemic to the Southwest Indian Ocean, where it inhabits a narrow continental shelf between an exposed coast and the upper reaches of the strong western-boundary Agulhas Current. Long-lived phyllosoma larvae released in this dynamic ocean environment have an uncertain fate—they can be retained over the shelf by sub-mesoscale processes, dispersed downstream along the coast or across the Mozambique Channel, or become entrained in the Agulhas Current, and presumably lost. To assess gene flow and population genetic structure, we analyzed mitochondrial cytochrome oxidase subunit 1 and hypervariable control region sequences, and 19 nuclear microsatellite loci obtained from lobsters collected at nine sites in eastern South Africa, Mozambique and southeast Madagascar. Clustering analyses confirmed genetic connectivity among all populations, and gene flow patterns supported the hypothesis that nearshore processes, such as lee eddies and counter currents, retain some phyllosomas over the shelf; whereas, net gene flow direction was moderate towards the southwest. The Mozambique Channel did not impede contemporary gene flow from Madagascar to the African shelf, but return gene flow was rare. Different marker types showed contrasting gene flow patterns during contemporary and evolutionary periods, when Pleistocene glacial/interglacial cycles would have affected sea level, ocean currents and dispersal patterns. Despite genetic connectivity and the importance of local recruitment, recent gene flow suggests an ancillary source/sink dynamic concordant with the prevailing southwesterly direction of boundary currents at the shelf-edge—a factor to consider in regional fisheries and conservation strategies.

Building the Tree of Life (ToL) is a major challenge of modern biology, requiring advances in cyberinfrastructure, data collection, theory, and more. Here, we argue that phylogenomics stands to benefit by embracing the many heterogeneous genomic signals emerging from the first decade of large-scale phylogenetic analysis spawned by high-throughput sequencing (HTS). Such signals include those most commonly encountered in phylogenomic datasets, such as incomplete lineage sorting, but also those reticulate processes emerging with greater frequency, such as recombination and introgression. Here we focus specifically on how phylogenetic methods can accommodate the heterogeneity incurred by such population genetic processes; we do not discuss phylogenetic methods that ignore such processes, such as concatenation or supermatrix approaches or supertrees. We suggest that methods of data acquisition and the types of markers used in phylogenomics will remain restricted until a posteriori methods of marker choice are made possible with routine whole-genome sequencing of taxa of interest. We discuss limitations and potential extensions of a model supporting innovation in phylogenomics today, the multispecies coalescent model (MSC). Macroevolutionary models that use phylogenies, such as character mapping, often ignore the heterogeneity on which building phylogenies increasingly rely and suggest that assimilating such heterogeneity is an important goal moving forward. Finally, we argue that an integrative cyberinfrastructure linking all steps of the process of building the ToL, from specimen acquisition in the field to publication and tracking of phylogenomic data, as well as a culture that values contributors at each step, are essential for progress. Funding Agencies|Chalmers University of Technology; University of Gothenburg; Swedish Research Council; U.S. National Science Foundation; European Research Council under the European Unions Seventh Framework Programme (FP/2007-2013, ERC) [331024]; Swedish Foundation for Strategic Research; Wallenberg Academy Fellowship; Conselho Nacional de Desenvolvimento Cientifico e Tecnologico-CNPq; U.S. National Academy of Sciences; U.S. Agency of International Development-PEER NAS/USAID; LOreal-Unesco For Women in Science Program

Macronycteris commersoni(Hipposideridae), a bat species endemic to Madagascar, is widespread across the island and utilizes a range of habitat types including open woodland, degraded habitats, and forested areas from sea level to 1,325 m. Despite being widely distributed, there is evidence thatM. commersoniexhibits morphological and bioacoustic variation across its geographical range. We investigated the fine-scale phylogeographic structure of populations in the western half of the island using extensive spatial sampling and sequence data from two mitochondrial DNA regions. Our results indicated several lineages withinM. commersoni.Individuals collected from northern Madagascar formed a single monophyletic clade (clade C). A second clade (clade B) included individuals collected from the south-western portion of the island. This second clade displayed more phylogeographical partitioning with differences in mtDNA haplotypes frequency detected between populations collected in different bioclimatic regions. Lineage dispersal, genetic divergence, and timing of expansion events ofM.commersoniwere probably associated with Pleistocene climate fluctuations. Our data suggest that the northern and the central western regions of Madagascar may have acted as refugia for this species during periods of cooler and drier climate conditions associated with the Pleistocene.

Full-length mitochondrial cytochrome c oxidase I (COI) sequence information from lobster phyllosoma larvae can be difficult to obtain when DNA is degraded or fragmented. Primers that amplify smaller fragments are also more useful in metabarcoding studies. In this study, we developed and tested a method to design a taxon-specific mini-barcode primer set for marine lobsters. The shortest, most informative portion of the COI gene region was identified in silico, and a DNA barcode gap analysis was performed to assess its reliability as species diagnostic marker. Primers were designed, and cross-species amplification success was tested on DNA extracted from a taxonomic range of spiny-, clawed-, slipper- and blind lobsters. The mini-barcode primers successfully amplified both adult and phyllosoma COI fragments, and were able to successfully delimit all species analyzed. Previously published universal primer sets were also tested and sometimes failed to amplify COI from phyllosoma samples. The newly designed taxon-specific mini-barcode primers will increase the success rate of species identification in bulk environmental samples and add to the growing DNA metabarcoding toolkit.

Populations of the Malagasy Hipposideros commersoni (family Hipposideridae) are threatened by deforestation and hunting. Maximum likelihood and Bayesian analysis of 148 cytochrome b sequences found this species to be paraphyletic and composed of three well-supported monophyletic clades. Clades B and C form a monophyletic lineage that can be referred to H. commersoni; these two clades are separated by 6% sequence variation. Clade A represents a distinct evolutionary lineage separate (9–11% average sequence divergence) from H. commersoni (clades B and C) and is named herein as a new species, Hipposideros cryptovalorona sp. nov. In the phylogeny presented herein, this species is strongly associated with the outgroup taxa Hipposideros gigas and Hipposideros vittatus, both restricted to Africa. External, cranial and dental measurements taken from the same individuals used in the molecular study indicate no clear distinction in morphology amongst these three clades; this includes noseleaf structure and craniodental characteristics. Principal component analyses showed limited separation of the three clades. Comparison to a Quaternary fossil species from north-west Madagascar, Hipposideros besaoka, found little morphological overlap between any of the three clades and this extinct species. Hence, at least three species of Hipposideros have occurred on Madagascar since the Late Pleistocene, two extant (H. commersoni s.s. and H. cryptovalorona sp. nov.) and one extinct (H. besaoka). © 2015 The Linnean Society of London

Human activity has facilitated the introduction of a number of alien mammal species to the Galápagos Archipelago. Understanding the phylogeographic history and population genetics of invasive species on the Archipelago is an important step in predicting future spread and designing effective management strategies. In this study, we describe the invasion pathway of Rattus rattus across the Galápagos using microsatellite data, coupled with historical knowledge. Microsatellite genotypes were generated for 581 R. rattus sampled from 15 islands in the archipelago. The genetic data suggest that there are at least three genetic lineages of R. rattus present on the Galápagos Islands. The spatial distributions of these lineages correspond to the main centers of human settlement in the archipelago. There was limited admixture among these three lineages, and these finding coupled with low rates of gene flow among island populations suggests that interisland movement of R. rattus is rare. The low migration among islands recorded for the species will have a positive impact on future eradication efforts.

Soils are integral to agricultural productivity, biodiversity, and the maintenance of ecosystem services. However, soil ecosystem research depends on foundational biological knowledge that is often missing. In this review, we present a comprehensive, cross-taxa overview of the soil biota of South Africa. We discuss the literature and sampling methods used to assess soil biota, the available taxonomic expertise and main collections within South Africa, the availability of identification guides and online resources, and the status and distribution of described species. We include species lists for all South African soil biota and, for groups with sufficient distribution records, species richness maps. Despite South Africa being only 0.8% of the earth’s terrestrial area, it contains nearly 1.8% of the world’s described soil species (mean per taxon 3.64%, range 0.17–15%; n = 36 groups), with nematodes and earthworms showing a remarkable (6.4 and 7.7%) proportion of globally described diversity. Endemism is high for most groups, ranging from 33–92%. However, major knowledge gaps exist for most soil biota groups. While sampling has been relatively comprehensive in some areas for a few groups (particularly those with direct socioeconomic impacts), the Nama-Karoo, Northern Cape and Eastern Cape are poorly sampled. Natural soils in biodiversity hotspots, such as the Fynbos Biome, are also understudied. We argue that a more integrative approach to acquiring foundational knowledge in soil biodiversity is needed if applied soil research is to be effective in ensuring sustainable soil health. Considerable investment will be required to bring our understanding of the soil biodiversity in this megadiverse region to a level where the Millennium Development Goals can be reached.

Earthworms are an important component of southern African invertebrate diversity, due both to their influential roles in soil ecosystems, and the relatively large number of species. As of 2010, there were 282 indigenous earthworm species (most endemic) known to South Africa belonging to three families: Microchaetidae, Tritogeniidae and Acanthodrilidae. In addition, 44 introduced species from six families had been recorded. However, earthworms are rarely included in environmental monitoring or conservation programmes—partly because sampling and species identification are difficult and many sampling methods are destructive and/or toxic. In this paper we review the earthworm sampling techniques most commonly used by screening data from a digitised literature collection on South African earthworms and on-line global searches. By examining a case study sampling of three vegetation types, this paper highlights taxonomic challenges and the effort required to properly curate specimens. The study provides...

Senecio madagascariensis Poiret (Asteraceae), an invasive herb from southern Africa that inflicts high economic losses in several countries worldwide, is currently a target for biological control in Australia and Hawaii. Several candidate insect agents were identified from the weed’s native range in South Africa. Confirmation of narrow host ranges, prior to agent importations into quarantine, is important for Australia given its rich native Senecio flora. In particular, surveys for candidate agents on closely related non-target plants in the native range can differentiate between host specific and unsuitable agents at an early stage. This study focused on endophagous insects from families that were deployed in biocontrol programmes against other weedy Asteraceae. The host-plant affinities of stem-boring Coleoptera and stem-boring and capitulum-feeding Lepidoptera and Diptera were assessed across 18 native herbaceous Senecio species in KwaZulu-Natal, South Africa. Since larval morphology is typically unable to confirm insect identity, DNA barcoding was used to differentiate between insect species associated with different Senecio species to determine their host-plant affinities. COI phylogenies revealed that stem-boring Curculionidae and Tortricidae and capitulum-feeding Pterophoridae and Tephritidae that are associated with S. madagascariensis were restricted to plants in the S. madagascariensis species complex. In contrast, none of the stem-boring Agromyzidae were restricted to S. madagascariensis or its species complex. This study has supported the selection of several potentially host-specific agents for S. madagascariensis that could be imported for quarantine testing in Australia and Hawaii.

Macronycteris commersonii (Hipposideridae), a bat species endemic to Madagascar, is widespread across the island, utilising open woodland, degraded habitats, and forested areas from sea level to 1325 m. We investigated the fine-scale phylogeographic history and relationships of populations occurring in the western half of the island using sequence data from two mitochondrial DNA regions and extensive geographical sampling. Our results indicated a highly supported monophyletic group of M. commersonii, in which the Northern Madagascar Clade C formed a single monophyletic clade. The most recent common ancestor of M. commersonii was dated to 0.82 million years ago (mid-Pleistocene). Population expansion events were inferred for Clade B from approximately 130,000 to 70,000 years BP. Bayesian clustering and AMOVA analyses inferred week population genetic structure and sequence data indicated that genetic subdivisions do not support an isolation-by-distance model. Lineage dispersal, genetic divergence, and expansion events of M. commersonii were likely to be associated with Pleistocene climate fluctuations. Our data suggested that the northern and the central western regions of Madagascar may have acted as refugia for this species during periods of cooler and drier climate conditions associated with the Pleistocene.

Building the Tree of Life (ToL) is a major challenge of modern biology, requiring major advances in cyberinfrastructure, data collection, theory, and more. Here, we argue that phylogenomics stands to benefit by embracing the many heterogeneous genomic signals emerging from the first decade of large-scale phylogenetic analysis spawned by High-throughput sequencing (HTS). Such signals include those most commonly encountered in phylogenomic datasets, such as incomplete lineage sorting, but also those reticulate processes emerging with greater frequency, such as recombination and introgression. We suggest that methods of data acquisition and the types of markers used in phylogenomics will remain restricted until a posteriori methods of marker choice are made possible with routine whole-genome sequencing of taxa of interest. We discuss limitations and potential extensions of a major model supporting innovation in phylogenomics today, the multispecies coalescent model. Macroevolutionary models that use phylogenies, such as character mapping, often ignore the heterogeneity on which building phylogenies increasingly rely, and suggest that assimilating such heterogeneity is an important goal moving forward. Finally, we argue that an integrative cyberinfrastructure linking all steps of the process of building the ToL, from specimen acquisition in the field to publication and tracking of phylogenomic data, as well as a culture that values contributors to each step, are essential for progress.