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opennotspecifiedSep 2020View details →

Figure 3 in A revision of pipistrelle-like bats (Mammalia: Chiroptera: Vespertilionidae) in East Africa with the description of new genera and species

Figure 3. Maximum likelihood phylogeny of mitochondrial cytochrome b sequences of Vespertilionidae: (A) Pipistrellus, Scotoecus, Vansonia, and outgroups (B) Afronycteris, Pseudoromicia, Nycticeinops, and Hypsugo (C) Laephotis and Neoromicia. The phylogeny was inferred in IQ-TREE, and its topology was similar to the Bayesian phylogeny calculated in MRBAYES. Filled red circles on nodes denote bootstrap (BS) values ≥ 70% and Bayesian posterior probabilities (PP) ≥ 0.95. Open circles outlined in black indicate BS ≥ 70% and PP <0.95, and open circles outlined in red indicate BS <70% and PP> 0.95. Support values for most minor clades are not shown. Specimen localities include counties for Kenya. DRC refers to Democratic Republic of the Congo and CAR to Central African Republic. Museum acronyms are defined in the Material and Methods section. Sequences downloaded from GenBank are indicated by inclusion of GenBank accession numbers (Supporting Information, Table S1). Branch colours indicate individual species/clade membership.

opennotspecifiedSep 2020View details →

Figure 1 in A revision of pipistrelle-like bats (Mammalia: Chiroptera: Vespertilionidae) in East Africa with the description of new genera and species

Figure 1. Type localities of taxa of African and Malagasy Vespertilionini and Pipistrellini. Valid species are denoted by filled circles, subspecies and synonyms by open circles and species described herein by stars: 1, Pipistrellus abaensis J. A. Allen, 1917; 2, N[ycticejus]. adovanus Heuglin, 1877; 3, Pipistrellus aero Heller, 1912; 4, Vespertilio pipistrellus var. africanus Rüppell, 1842; 5, Nycticeius africanus G. M. Allen, 1911; 6, Scotoecus albigula Thomas, 1909; 7, Scoteinus schlieffeni albiventer Thomas & Wroughton, 1908; 8, Scotophilus albofuscus Thomas, 1890; 9, Vesperugo anchietae Seabra, 1900; 10, Laephotis angolensis Monard, 1935; 11, Eptesicus capensis angolensis Hill, 1937; 12, Pipistrellus ariel Thomas, 1904; 13, Scotoecus artinii De Beaux, 1923; 14, Eptesicus ater J. A. Allen, 1917; 15, Pipistrellus nanus australis Roberts, 1913; 16, Scoteinus schlieffeni australis Thomas & Wroughton, 1908; 17, Scoteinus schlieffeni bedouin Thomas & Wroughton, 1908; 18, Pipistrellus eisentrauti bellieri De Vree, 1972; 19, Hypsugo bemainty Goodman et al., 2015; 20, Vesperus bicolor Bocage, 1889; 21, Laephotis botswanae Setzer, 1971; 22, Pipistrellus (Romicia) kuhlii broomi Roberts, 1948; 23, Vesperugo (Vesperus) brunneus Thomas, 1880; 24, Vespertilio capensis A. Smith, 1829; 25, Scotoecus cinnamomeus Wettstein, 1916; 26, Pipistrellus crassulus Thomas, 1904; 27, Pipistrellus culex Thomas, 1911; 28, Vesperus damarensis Noack, 1889; 29, Scotophilus darwini Tomes, 1859; 30, Pipistrellus deserti Thomas, 1902; 31, Pipistrellus eisentrauti Hill, 1968; 32, Scotoecus falabae Thomas, 1915; 33, Eptesicus faradjius J. A. Allen, 1917; 34, Scoteinus schlieffeni fitzsimonsi Roberts, 1932; 35, Pipistrellus fouriei Thomas, 1926; 36, Pipistrellus kuhlii fuscatus Thomas, 1901; 37, Pipistrellus fuscipes Thomas, 1913; 38, Eptesicus garambae J. A. Allen, 1917; 39, Vespertilio capensis gracilior Thomas & Schwann, 1905; 40, Vesperugo (Vesperus) grandidieri Dobson, 1876; 41, Vesperus guineensis Bocage, 1889; 42, Pipistrellus hanaki Hulva & Benda, 2004; 43, Parahypsugo happoldorum Hutterer, Decher, Monadjem & Astrin, 2019; 44, Pipistrellus helios Heller, 1912; 45, Vespertilio hesperida Temminck, 1840; 46, Scotoecus hindei Thomas, 1901; 47, Scotophilus hirundo de Winton, 1899; 48, Vesperus humbloti Milne-Edwards, 1881; 49, Vesperugo hypoleucus Heuglin [in Fitzinger & Heuglin], 1866; 50, Pipistrellus inexspectatus Aellen, 1959; 51, Neoromicia isabella Decher, Hutterer & Monadjem, 2016; 52, Laephotis kirinyaga Monadjem et al., this paper; 53, Pseudoromicia kityoi Monadjem et al., this paper; 54, Hypsugo lanzai Benda, Al-Jumaily, Reiter & Nasher, 2011; 55, Pipistrellus leucomelas Monard, 1932; 56, Parahypsugo macrocephalus Hutterer & Kerbis Peterhans, 2019; 57, Vesperugo maderensis Dobson, 1878; 58, Eptesicus somalicus malagasyensis Peterson, Eger & Mitchell, 1995; 59, Vespertilio marginatus Cretzschmar, 1830; 60, Pipistrellus marrensis Thomas & Hinton, 1923; 61, Vespertilio matroka Thomas & Schwann, 1905; 62, Pipistrellus africanus meesteri Kock, 2001; 63, Eptesicus melckorum Roberts, 1919; 64, Scotophilus minimus Noack, 1887; 65, Pipistrellus minusculus Miller, 1900; 66, Vespertilio minuta Temminck, 1840; 67, Pipistrella minuta Loche, 1867; 68, Pipistrellus musciculus Thomas, 1913; 69, Laephotis namibensis Setzer, 1971; 70, Pipistrellus nanulus Thomas, 1904; 71, Vespertilio nanus Peters, 1852; 72, Eptesicus capensis nkatiensis Roberts, 1932; 73, Scabrifer notius G. M. Allen, 1908; 74, Pseudoromicia nyanza Monadjem et al., this paper; 75, †Scotoecus olduvensis Gunnell, Butler, Greenwood & Simmons, 2015; 76, Vesperugo pagenstecheri Noack, 1889; 77, Pipistrellus (Pipistrellus) permixtus Aellen, 1957; 78, Eptesicus phasma G. M. Allen, 1911; 79, Vespertilio pipistrellus Schreber, 1774; 80, Vespertilio platycephalus Temminck, 1832; 81, Vesperugo pulcher Dobson, 1875; 82, Vesperugo pusillulus Peters, 1870; 83, Pipistrellus raceyi Bates et al., 2006; 84, Eptesicus rectitragus Wettstein, 1916; 85, Vesperugo (Vesperus) rendalli Thomas, 1889; 86, Neoromicia robertsi Goodman et al., 2012; 87, Neoromicia roseveari Monadjem et al., 2013; 88, V[espertilio]. rueppelii J. Fischer, 1829; 89, Scotophilus rusticus Tomes, 1861; 90, Vespertilio savii Bonaparte, 1837; 91, Nycticejus schlieffenii Peters, 1859; 92, Pipistrellus rueppelli senegalensis Dorst, 1960; 93, †Nycticeinops serengetiensis Gunnell et al., 2015; 94, Pipistrellus simandouensis Monadjem et al., 2020; 95, Vespertilio minutus somalicus Thomas, 1901; 96, Vesperugo stampflii Jentink, 1888; 97, Neoromicia stanleyi Goodman et al., 2017; 98, Vesperus tenuipinnis Peters, 1872; 99, Eptesicus ugandae Hollister, 1916; 100, Neoromicia vansoni Roberts, 1932; 101, Pipistrellus vernayi Roberts, 1932; 102, Laephotis wintoni Thomas, 1901; 103, Scotoecus woodi Thomas, 1917; 104, Eptesicus zuluensis Roberts, 1924. Not mapped: [Pipistrellus Kuhli] latastei Laurent, 1937; Vespertilio pusillus LeConte, 1857; Vesperugo subtilis Sundevall, 1846.

opencc-zeroMar 2020View details →

Description and classification of echolocation clicks of Indian Ocean humpback (Sousa plumbea) and Indo-Pacific bottlenose (Tursiops aduncus) dolphins from Menai Bay, Zanzibar, East Africa

<p>Passive acoustic monitoring (PAM) is a powerful method to study the occurrence, movement and behavior of echolocating odontocetes (toothed whales) in the wild. However, in areas occupied by more than one species, echolocation clicks need to be classified into species. The present study investigated whether the echolocation clicks produced by small, at-risk, resident sympatric populations of Indian Ocean humpback dolphin (Sousa plumbea) and Indo-Pacific bottlenose dolphin (Tursiops aduncus) in Menai Bay, Zanzibar, East Africa, could be classified to allow species specific monitoring. Underwater sounds of S. plumbea and T. aduncus groups were recorded using a SoundTrap 202HF in January and June-August 2015. Eight acoustic parameters, i.e. -10 dB duration, peak, centroid, lower -3 and lower -10 dB frequencies, and -3 dB, -10 dB and root-mean-squared bandwidth, were used to describe and compare the two species' echolocation clicks. Statistical analyses showed that S. plumbea clicks had significantly higher peak, centroid, lower -3 and lower -10 dB frequencies compared to T. aduncus, whereas duration and bandwidth parameters were similar for the two species. Random Forest (RF) classifiers were applied to determine parameters that could be used to classify the two species from echolocation clicks and achieved 28.6% and 90.2% correct species classification rates for S. plumbea and T. aduncus, respectively. <a name="_Hlk32088545">Both species were classified at a higher rate than expected at random, however the identified classifiers would only be useful for T. aduncus monitoring.</a> <a name="_Hlk32088580">The frequency and bandwidth parameters provided most power for species classification.</a> <a name="_Hlk32088592">Further study is necessary to identify useful classifiers for S. plumbea.</a> This study represents a first step in acoustic <a name="_Hlk32088605">description </a>and classification of S. plumbea and T. aduncus in the western Indian Ocean region, with potential application for future acoustic monitoring of species-specific temporal and spatial occurrence in these sympatric species.</p>

opencc-zeroDec 2016View details →

Data from: A chromosome 5q31.1 locus associates with tuberculin skin test reactivity in HIV-positive individuals from tuberculosis hyper-endemic regions in east Africa

One in three people has been infected with Mycobacterium tuberculosis (MTB), and the risk for MTB infection in HIV-infected individuals is even higher. We hypothesized that HIV-positive individuals living in tuberculosis-endemic regions who do not get infected by Mycobacterium tuberculosis are genetically resistant. Using an "experiment of nature" design that proved successful in our previous work, we performed a genome-wide association study of tuberculin skin test positivity using 469 HIV-positive patients from prospective study cohorts of tuberculosis from Tanzania and Uganda to identify genetic loci associated with MTB infection in the context of HIV-infection. Among these individuals, 244 tested were tuberculin skin test (TST) positive either at enrollment or during the >8 year follow up, while 225 were not. We identified a genome-wide significant association between the dominant model of rs877356 and binary TST status in the combined cohort (OR=0.2671, p=1.22x10-8). Association was replicated with similar significance when examining TST induration as a continuous trait. The variant lies in the 5q31.1 region, 57kb downstream from IL9. Two-locus analyses of association of variants near rs877356 showed a haplotype comprised of rs877356 and an IL9 missense variant rs2069885 had the most significant association (p=1.59x10-12). We also replicated previously linked loci on chromosomes 2, 5, and 11. IL9 is a cytokine produced by mast cells and T¬H2 cells during inflammatory responses, providing a possible link between airway inflammation and protection from MTB infection. Our results indicate that studying uninfected participants with extensive exposure increases the power to detect associations in complex infectious disease.

opencc-zeroDec 2014View details →

Data from: Quantitative genetic analyses of male color pattern and female mate choice in a pair of cichlid fishes of Lake Malawi, East Africa

The traits involved in sexual selection, such as male secondary sexual characteristics and female mate choice, often co-evolve which can promote population differentiation. However, the genetic architecture of these phenotypes can influence their evolvability and thereby affect the divergence of species. The extraordinary diversity of East African cichlid fishes is often attributed to strong sexual selection and thus this system provides an excellent model to test predictions regarding the genetic architecture of sexually selected traits that contribute to reproductive isolation. In particular, theory predicts that rapid speciation is facilitated when male sexual traits and female mating preferences are controlled by a limited number of linked genes. However, few studies have examined the genetic basis of male secondary sexual traits and female mating preferences in cichlids and none have investigated the genetic architecture of both jointly. In this study, we artificially hybridized a pair of behaviorally isolated cichlid fishes from Lake Malawi and quantified both melanistic color pattern and female mate choice. We investigated the genetic architecture of both phenotypes using quantitative genetic analyses. Our results suggest that 1) many non-additively acting genetic factors influence melanistic color patterns, 2) female mate choice may be controlled by a minimum of 1–2 non-additive genetic factors, and 3) F2 female mate choice is not influenced by male courting effort. Furthermore, a joint analysis of color pattern and female mate choice indicates that the genes underlying these two traits are unlikely to be physically linked. These results suggest that reproductive isolation may evolve rapidly owing to the few genetic factors underlying female mate choice. Hence, female mate choice likely played an important role in the unparalleled speciation of East African cichlid fish.

opencc-zeroDec 2014View details →

Data from: Eco-morphological differentiation in Lake Magadi tilapia, an extremophile cichlid fish living in hot, alkaline and hypersaline lakes in East Africa

Ecological diversification through divergent selection is thought to be a major force during the process of adaptive radiations. However, the large sizes and complexity of most radiations such as those of the cichlids in the African Great Lakes make it impossible to infer the exact evolutionary history of any population divergence event. The genus Alcolapia, a small cichlid lineage endemic to Lakes Magadi and Natron in East Africa, exhibits phenotypes similar to some of those found in cichlids of the radiations of the African Great Lakes. The simplicity within Alcolapia makes it an excellent model system to investigate ecological diversification and speciation. We used an integrated approach including population genomics based on RAD-seq data, geometric morphometrics, and stable isotope analyses to investigate the eco-morphological diversification of tilapia in Lake Magadi and its satellite lake Little Magadi. Additionally, we reconstructed the demographic history of the species using coalescent simulations based on the joint site frequency spectrum. The population in Little Magadi has a characteristically upturned mouth - possibly an adaptation to feeding on prey from the water surface. Eco-morphological differences between populations within Lake Magadi are more subtle, but are consistent with known ecological differences between its lagoons such as high concentrations of nitrogen attributable to extensive guano deposits in Rest of Magadi relative to Fish Springs Lagoon. All populations diverged simultaneously only about 1,100 generations ago. Differences in levels of gene flow between populations and the effective population sizes have likely resulted in the inferred heterogeneous patterns of genome-wide differentiation.

opennotspecifiedDec 2004View details →

FIGURE 1 in A new species of Strongylodesma Lévi, 1969 (Porifera; Demospongiae; Poecilosclerida; Latrunculiidae) from Aliwal Shoal on the east coast of South Africa

FIGURE 1. Map of collection locality on the east coast of South Africa. Aliwal Shoal is situated about 5km off the town of Umkomaas on the KwaZuluNatal South Coast, about 45 minutes drive from Durban.

opennotspecifiedDec 2004View details →

FIGURE 2. A in A new species of Strongylodesma Lévi, 1969 (Porifera; Demospongiae; Poecilosclerida; Latrunculiidae) from Aliwal Shoal on the east coast of South Africa

FIGURE 2. A. Gross morphology of Strongylodesma aliwaliensis sp. nov. (SAM H5083); B. A close up frame of the fungiform areolate porefields and cylindrical oscules of Strongylodesma aliwaliensis sp. nov. (SAM H5083); C. Smooth anisostrongyles with one end narrower within Strongylodesma aliwaliensis sp. nov. (Anisostrongyles) (1000 X).

opennotspecifiedDec 2004View details →

FIGURE 3A, C in A new species of Strongylodesma Lévi, 1969 (Porifera; Demospongiae; Poecilosclerida; Latrunculiidae) from Aliwal Shoal on the east coast of South Africa

FIGURE 3A, C. Skeletal architecture of the holotype (SAM H5083) (A, 100 X; C, 50 X); C. Skeletal architecture showing the clear mesohyl region below the paratangential layer of anisostrongyles (100 X); B. Skeletal architecture of the paratype (SAF 9423) (50 X); D. Skeletal architecture showing the region of convoluted tracts of anisostrongyles (100 X).

FIGURE 4 in A new species of Calappa Weber, 1795 (Crustacea: Decapoda: Calappidae) from East and South Africa

FIGURE 4. Calappa africana, new species, male holotype (81.2 by 109.7 mm) (USNM 268804). A, left G1; B, distal part of left G1; C, left G2; D, abdomen; E, first article of antenna. Scale: 1mm

FIGURE 3 in A new species of Calappa Weber, 1795 (Crustacea: Decapoda: Calappidae) from East and South Africa

FIGURE 3. External margin of merus of left cheliped. A, Calappa africana, new species, male holotype (81.2 by 109.7 mm) (USNM 268804); B, Calappa japonica, female (74.6 by 100.1 mm) (ZRC 2006.0113).

FIGURE 2 in A new species of Calappa Weber, 1795 (Crustacea: Decapoda: Calappidae) from East and South Africa

FIGURE 2. Frontal views. Calappa africana, new species: A, male holotype (81.2 by 109.7 mm) (USNM 268804); B, female paratype (80.5 by 105.8 mm) (ZRC 2006.0109); Calappa japonica: C, male (94.24 by 131.3mm) (ZRC 2001.002); D, female (74.6 by 100.1 mm) (ZRC 2006.0113).

FIGURE 1. A, B in A new species of Calappa Weber, 1795 (Crustacea: Decapoda: Calappidae) from East and South Africa

FIGURE 1. A, B, Calappa africana, new species, male holotype (81.2 by 109.7 mm) (USNM 268804); C, D, Calappa africana female paratype (80.5 by 105.8 mm) (ZRC 2006.0109); E, F, Calappa japonica, female (74.6 by 100.1 mm) (ZRC 2006.0113). A, C, E, dorsal view of carapace; B, D, F, left cheliped, external surface.

FIGURE 15 in New species and new records of dendrochirotid and dactylochirotid holothuroids (Echinodermata: Holothuroidea) from off the east coast of South Africa

FIGURE 15. Psolidothuria yasmeena sp. nov. Holotype. SAMA279134. A. scales from midlateral body wall; B. endplate from ventrolateral podium; C. plates and rod from ventrolateral podia; D. rods from tentacle stalk; E. plates from tentacle tip; F. plates from introvert; G. internal anatomy; H. largest tentacle; I. calcareous ring. (CR—calcareous ring; pv—Polian vesicle). A scale a; B–F scale b; H–I scale c.

FIGURE 14 in New species and new records of dendrochirotid and dactylochirotid holothuroids (Echinodermata: Holothuroidea) from off the east coast of South Africa

FIGURE 14. Ekkentropelma groovia sp. nov. Holotype. SAMA27913. A. plates from dorsolateral body wall; B. plates from sole; C. plates and rod from dorsolateral podia; D. plates and rods from ventral podia; E. endplate from ventral podium; F. rods from tentacles; G. single tentacle; H. calcareous ring and associated structures; I. whole animal. A–F scale a; G & H scale b.

FIGURE 13 in New species and new records of dendrochirotid and dactylochirotid holothuroids (Echinodermata: Holothuroidea) from off the east coast of South Africa

FIGURE 13. Psolidium acorbulum sp. nov. Holotype. SAMA27911. A. scale from dorsolateral body wall; B. scale from dorsal body wall; C. plates from ventral body wall; D. plates from dorsal podia; E. rods/plates from ventrolateral podia; F. endplate from the ventrolateral podium; G. rods from tentacle stalk; H. rods from tentacle branches and tips; I. calcareous ring showing midventral radial plate; J. dorsal radial plate; K. single tentacle; L. polian vesicle and stone canal; M. Paratype. SAMA27912, entire. A & B scale a; C–H scale b; I–K scale c.

FIGURE 11 in New species and new records of dendrochirotid and dactylochirotid holothuroids (Echinodermata: Holothuroidea) from off the east coast of South Africa

FIGURE 11. Staurothyone rosacea (Semper, 1869). SAMA27910. A. crosses from body wall; B. rosettes from body wall; C. calcareous ring.

FIGURE 10 in New species and new records of dendrochirotid and dactylochirotid holothuroids (Echinodermata: Holothuroidea) from off the east coast of South Africa

FIGURE 10. Plesiocolochirus tessellarus (Cherbonnier, 1970). SAM27909. A. largeknobbed buttons from dorsal body wall; B. side view of buttons; C. plate/scale from dorsal body wall; D. baskets from dorsal body wall; E. side view of baskets from dorsal body wall; F. baskets from dorsal podia; G. rods from dorsal podia; H. smallknobbed plates from dorsal podia; I. endplate from dorsal podium; J. part of endplate from ventral podium; K. plates from tentacles; L. tentacle rods. AC & GL scale a; DF scale b.

FIGURE 12 in New species and new records of dendrochirotid and dactylochirotid holothuroids (Echinodermata: Holothuroidea) from off the east coast of South Africa

FIGURE 12. Psolidium multipes sp. nov. Holotype. SAMA23175. A. scale from dorsal body wall; B. largeknobbed buttons from ventral body wall; C. smallknobbed buttons from ventral body wall; D. plates from ventral podia; E. rosettes from ventral body wall; F. closed baskets from ventral body wall; G. open baskets from dorsal podia; H. rods and plates from tentacle branches and tips; I. rods from tentacle stalk; J. endplate from ventral podium; K. stone canal (frontal and lateral view); L. calcareous ring. B–J scale a.

FIGURE 9 in New species and new records of dendrochirotid and dactylochirotid holothuroids (Echinodermata: Holothuroidea) from off the east coast of South Africa

FIGURE 9. Plesiocolochirus dispar (Lampert, 1889).SAMA23175. A. dorsal body wall scales; B. smallknobbed buttons; C. largeknobbed buttons; D. part of endplate from ventral podia; E. closed baskets from dorsal body wall; F. smooth plates from dorsal podium; G. knobbed plates from dorsal podium; H. small rods from tentacles; I. rosettes from tentacles; J. large rods from tentacle stalk; K. madreporite; L. calcareous ring. B–H & J scale a; I scale b.