1,721,005 research outputs found
Exploring rain forest diversification using demographic model testing in the African foam‐nest treefrog Chiromantis rufescens
No full textAim
Species with wide distributions spanning the African Guinean and Congolian rain forests are often composed of genetically distinct populations or cryptic species with geographic distributions that mirror the locations of the remaining forest habitats. We used phylogeographic inference and demographic model testing to evaluate diversification models in a widespread rain forest species, the African foam‐nest treefrog Chiromantis rufescens.
Location
Guinean and Congolian rain forests, West and Central Africa.
Taxon
Chiromantis rufescens.
Methods
We collected mitochondrial DNA (mtDNA) and single‐nucleotide polymorphism (SNP) data for 130 samples of C. rufescens. After estimating population structure and inferring species trees using coalescent methods, we tested demographic models to evaluate alternative population divergence histories that varied with respect to gene flow, population size change and periods of isolation and secondary contact. Species distribution models were used to identify the regions of climatic stability that could have served as forest refugia since the last interglacial.
Results
Population structure within C. rufescens resembles the major biogeographic regions of the Guinean and Congolian forests. Coalescent‐based phylogenetic analyses provide strong support for an early divergence between the western Upper Guinean forest and the remaining populations. Demographic inferences support diversification models with gene flow and population size changes even in cases where contemporary populations are currently allopatric, which provides support for forest refugia and barrier models. Species distribution models suggest that forest refugia were available for each of the populations throughout the Pleistocene.
Main conclusions
Considering historical demography is essential for understanding population diversification, especially in complex landscapes such as those found in the Guineo–Congolian forest. Population demographic inferences help connect the patterns of genetic variation to diversification model predictions. The diversification history of C. rufescens was shaped by a variety of processes, including vicariance from river barriers, forest fragmentation and adaptive evolution along environmental gradient
Idiosyncratic responses to climate-driven forest fragmentation and marine incursions in reed frogs from Central Africa and the Gulf of Guinea Islands
No full textOrganismal traits interact with environmental variation to mediate how species respond to shared landscapes. Thus, differences in traits related to dispersal ability or physiological tolerance may result in phylogeographic discordance among co-distributed taxa, even when they are responding to common barriers. We quantified climatic suitability and stability, and phylogeographic divergence within three reed frog species complexes across the Guineo-Congolian forests and Gulf of Guinea archipelago of Central Africa to investigate how they responded to a shared climatic and geological history. Our species-specific estimates of climatic suitability through time are consistent with temporal and spatial heterogeneity in diversification among the species complexes, indicating that differences in ecological breadth may partly explain these idiosyncratic patterns. Likewise, we demonstrated that fluctuating sea levels periodically exposed a land bridge connecting Bioko Island with the mainland Guineo-Congolian forest and that habitats across the exposed land bridge likely enabled dispersal in some species, but not in others. We did not find evidence that rivers are biogeographic barriers across any of the species complexes. Despite marked differences in the geographic extent of stable climates and temporal estimates of divergence among the species complexes, we recovered a shared pattern of intermittent climatic suitability with recent population connectivity and demographic expansion across the Congo Basin. This pattern supports the hypothesis that genetic exchange across the Congo Basin during humid periods, followed by vicariance during arid periods, has shaped regional diversity. Finally, we identified many distinct lineages among our focal taxa, some of which may reflect incipient or unrecognized specie
Two new species of long-fingered frogs of the genus Cardioglossa (Anura: Arthroleptidae) from Central African rainforests
No full textWe describe two new frog species of Cardioglossa (Family Arthroleptidae) from
Central Africa. The new species are found in the rainforests of western-central Democratic
Republic of the Congo and the Republic of the Congo near the Gabonese border, respectively.
We demonstrate that these species are morphologically and genetically distinct from each other
and all other species of Cardioglossa. Both new species lack the dorsal hour-glass pattern
present in many species of the genus, but they can be distinguished from each other and related
species by distinctive colour patterns on their lateral surfaces and extremities. Both new species
most closely resemble C. gratiosa, which occurs in the Atlantic coastal forests extending from
Cameroon through Gabon. The new species can be differentiated from C. gratiosa by the
absence of black transverse bars on all limbs or by distinctive lateral colouration. Analysis of
mitochondrial ribosomal 16S DNA sequences reveals low to moderate levels (1.9–7.5%) of
divergence between these new species and closely related species of Cardioglossa. The
floodplains of the Congo and Ubangi Rivers may be important geographic barriers for many of
these species. The occurrence of these two new lowland species in the Congo Basin reveals that
the distribution and diversity of Cardioglossa in this region was underestimated. In addition,
we elevate C. nigromaculata inornata to species-level status, based in part on newly available
colour photographs from 1950 of specimens from the only known localit
Diversity and biogeography of frogs in the genus Amnirana (Anura: Ranidae) across sub-Saharan Africa
No full textFrogs in the genus Amnirana (family Ranidae) are widely distributed across sub-Saharan Africa and present a model system for exploring the relationship between diversification and geography across the continent. Using multiple loci from the mitochondrial (16S) and nuclear genomes (DISP2, FICD, KIAA2013, REV3L), we generated a strongly supported species-level phylogeny that provides insights into the continental biogeography of African species of Amnirana, which form a monophyletic group within the genus. Species delimitation analyses suggest that there may be as many as seven additional species of Amnirana in Africa. The biogeographic history of Amnirana is marked by several dispersal and vicariance events, including dispersal from the Lower Guinean Forest into the Congo Basin. In addition, phylogeographic patterns within two widespread species, A. albolabris and A. galamensis, reveal undescribed cryptic diversity. Populations assigned to A. albolabris in western Africa are more closely related to A. fonensis and require recognition as a distinct species. Our analyses reveal that the Lower and Upper Guinean Forest regions served as important centers of interspecific and intraspecific diversifications for Amniran
A phylogeny and genus-level revision of the African file snakes Gonionotophis Boulenger (Squamata: Lamprophiidae)
No full textThe sub-Saharan African file snake genus
Gonionotophis
is currently
comprised of 15 species. However, the concept of this genus has
been confounded by morphological and genetic differences
between the constituent taxa. Due to the dearth of DNA samples,
a taxonomic assessment has been impractical to date. We
therefore sequenced two mitochondrial and one nuclear marker
(16S, cyt
b
, and c-mos) from 45 samples representing ten species
of
Gonionotophis
to construct a molecular phylogeny using
Bayesian and likelihood approaches. Four divergent and well-
supported clades were recovered, including: (1)
grantii
+
brussauxi
;
(2)
poensis
+
stenophthalmus
; (3)
nyassae
; and (4)
capensis
,
chanleri
,
crossi
,
guirali
and
savorgnani
. Based on these results and
morphological data, the genus
Gonionotophis
is restricted to the
first clade,
Mehelya
is resurrected for the species in the second
clade, and new genera are described for the remaining two clade
Evolutionary history of burrowing asps (Lamprophiidae: Atractaspidinae) with emphasis on fang evolution and prey selection
Full text linkAtractaspidines are poorly studied, fossorial snakes that are found throughout Africa and western Asia, including the Middle East. We employed concatenated gene-tree analyses and divergence dating approaches to investigate evolutionary relationships and biogeographic patterns of atractaspidines with a multi-locus data set consisting of three mitochondrial (16S, cyt b, and ND4) and two nuclear genes (c-mos and RAG1). We sampled 91 individuals from both atractaspidine genera (Atractaspis and Homoroselaps). Additionally, we used ancestral-state reconstructions to investigate fang and diet evolution within Atractaspidinae and its sister lineage (Aparallactinae). Our results indicated that current classification of atractaspidines underestimates diversity within the group. Diversification occurred predominantly between the Miocene and Pliocene. Ancestral-state reconstructions suggest that snake dentition in these taxa might be highly plastic within relatively short periods of time to facilitate adaptations to dynamic foraging and life-history strategie
Phylogeny and biogeography of the African burrowing snake subfamily Aparallactinae (Squamata: Lamprophiidae)
No full textMembers of the snake subfamily Aparallactinae occur in various habitats throughout sub-Saharan Africa. The monophyly of aparallactine snakes is well established, but relationships within the subfamily are poorly known. We sampled 158 individuals from six of eight aparallactine genera in sub-Saharan Africa. We employed concatenated gene-tree analyses, divergence dating approaches, and ancestral-area reconstructions to infer phylogenies and biogeographic patterns with a multi-locus data set consisting of three mitochondrial (16S, cyt b, and ND4) and two nuclear genes (c-mos and RAG1). As a result, we uncover several cryptic lineages and elevate a lineage of Polemon to full species status. Diversification occurred predominantly during the Miocene, with a few speciation events occurring subsequently in the Pliocene and Pleistocene. Biogeographic analyses suggested that the Zambezian biogeographic region, comprising grasslands and woodlands, facilitated radiations, vicariance, and dispersal for many aparallactines. Moreover, the geographic distributions of many forest species were fragmented during xeric and cooler conditions, which likely led to diversification events. Biogeographic patterns of aparallactine snakes are consistent with previous studies of other sub-Saharan herpetofaun
Diversifying into the branches: species boundaries in African green and bush snakes, Philothamnus (Serpentes: Colubridae)
No full textThe African green and bush snakes of the genus Philothamnus currently comprises 21 species and three subspecies and occurs throughout sub-Saharan Africa. The genus has been the subject of previous taxonomic revisions based on traditional morphological characters and limited genetic assessment, and may not reflect their evolutionary history. Indeed, previous findings based on phylogenetics show discordant results of interspecific relationships and question the monophyly of the genus, although taxon sampling has been limited to date. We investigated phylogenetic affinities within Philothamnus with more inclusive genetic and geographical sampling, with the aim of better understanding their evolutionary history, so that future taxonomic revision of Philothamnus can be better informed. Species relationships were examined within a phylogenetic context and sampling included 133 ingroup samples from 16 taxa. Phylogenies were constructed in Bayesian and likelihood frameworks using three mitochondrial (16S, cyt b and ND4) and two nuclear (c-mos and RAG1) markers. Competing hypotheses relating to the monophyly of the genus were tested with a Shimodaira-Hasegawa test. To examine species boundaries, Bayesian General Mixed Yule-Coalescent Model and multi-rate Poisson Tree Processes analyses were conducted. In addition, a barcoding approach was used to further clarify species-level relationships by comparing frequency distributions between intra- and interspecific sequence divergence. The genus was recovered as monophyletic; however, species-delimitation results suggest that the current taxonomy does not reflect the evolutionary history of this group. For example, Philothamnus s. semivariegatus is paraphyletic, with at least four distinct clades. Philothamnus carinatus consists of two cryptic (sister) lineages from Central and West Africa that are deeply divergent, suggesting a long history of isolation between those regions. Furthermore, the subspecies P. n. natalensis and P. n. occidentalis show strong support for species-level divergence, which reflects their morphological and ecological differences. Accordingly, we elevate P. occidentalisnov. comb. to a full species. A fully informed taxonomic revision of these taxa will require additional morphological and ecological data for corroboration, but it seems that the morphological characters (e.g. scalation, dentition) used to describe these species to date are labile within and between species. This most likely has clouded our understanding of the species boundaries within the genus. Our phylogeny and species-delimitation analyses should provide a sounder framework for taxonomy, but may also prove useful toward understanding the morphological adaptations of these species to their respective habitat
Sky, sea, and forest islands: diversification in the African leaf‐folding frog Afrixalus paradorsalis (Anura: Hyperoliidae) of the Lower Guineo‐Congolian rain forest
No full textAim
To investigate how putative barriers, forest refugia, and ecological gradients across the lower Guineo‐Congolian rain forest shape genetic and phenotypic divergence in the leaf‐folding frog Afrixalus paradorsalis, and examine the role of adjacent land bridge and sky‐islands in diversification.
Location
The Lower Guineo‐Congolian Forest, the Cameroonian Volcanic Line (CVL), and Bioko Island, Central Africa.
Taxon
Afrixalus paradorsalis (Family: Hyperoliidae), an African leaf‐folding frog.
Methods
We used molecular and phenotypic data to investigate diversity and divergence among the A. paradorsalis species complex distributed across lowland rain forests, a land bridge island, and mountains in Central Africa. We examined the coincidence of population boundaries, landscape features, divergence times, and spatial patterns of connectivity and diversity, and subsequently performed demographic modelling using genome‐wide SNP variation to distinguish among divergence mechanisms in mainland (riverine barriers, forest refugia, ecological gradients) and land bridge island populations (vicariance, overwater dispersal).
Results
We detected four genetically distinct allopatric populations corresponding to Bioko Island, the CVL, and two lowland rain forest populations split by the Sanaga River. Although lowland populations are phenotypically indistinguishable, pronounced body size evolution occurs at high elevation, and the timing of the formation of the high elevation population coincides with mountain uplift in the CVL. Spatial analyses and demographic modelling revealed population divergence across mainland Lower Guinea is best explained by forest refugia rather than riverine barriers or ecological gradients, and that the Bioko Island population divergence is best explained by vicariance (marine incursion) rather than overseas dispersal.
Main conclusions
We provide growing support for the important role of forest refugia in driving intraspecific divergences in the Guineo‐Congolian rain forest. In A. paradorsalis, sky‐islands in the CVL have resulted in greater genetic and phenotypic divergences than marine incursions of the land bridge Bioko Island, highlighting important differences in patterns of island‐driven diversification in Lower Guine
FIGURE 1 in A molecular phylogeny of African Dainty Frogs, with the description of four new species (Anura: Pyxicephalidae: Cacosternum)
No full textFIGURE 1. Phylogeny of Cacosternum species, based on 16S. Branch support is indicated as Posterior Probability/Maximum Likelihood Bootstrap. Terminal triangles represent collapsed clades, to simplify the tree. Numerals in parentheses represent sample size/number of localities.Published as part of Channing, Alan, Schmitz, Andreas, Burger, Marius & Kielgast, Jos, 2013, A molecular phylogeny of African Dainty Frogs, with the description of four new species (Anura: Pyxicephalidae: Cacosternum), pp. 518-550 in Zootaxa 3701 (5) on page 521, DOI: 10.11646/zootaxa.3701.5.2, http://zenodo.org/record/21705
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