Cryptic diversity and species boundaries within the Paragalago zanzibaricus species complex

Cryptic species conservation: a review

Cryptic species are groups of two or more taxa that were previously classified as single nominal species. Being almost morphologically indistinguishable, cryptic species have historically been hard to detect. Only through modern morphometric, genetic, and molecular analyses has the hidden biodiversity of cryptic species complexes been revealed. Cryptic diversity is now widely acknowledged, but unlike more recognisable, charismatic species, scientists face additional challenges when studying cryptic taxa and protecting their wild populations. Demographical and ecological data are vital to facilitate and inform successful conservation actions, particularly at the individual species level, yet this information is lacking for many cryptic species due to their recent taxonomic description and lack of research attention. The first part of this article summarises cryptic speciation and diversity, and explores the numerous barriers and considerations that conservation biologists must navigate to detect, study and manage cryptic species populations effectively. The second part of the article seeks to address how we can overcome the challenges associated with efficiently and non-invasively detecting cryptic species in-situ, and filling vital knowledge gaps that are currently inhibiting applied conservation. The final section discusses future directions, and suggests that large-scale, holistic, and collaborative approaches that build upon successful existing applications will be vital for cryptic species conservation. This article also acknowledges that sufficient data to implement effective species-specific conservation will be difficult to attain for many cryptic animals, and protected area networks will be vital for their conservation in the short term.

Phylogeography and evolutionary lineage diversity in the small-eared greater galago, Otolemur garnettii (Primates: Galagidae)

Assessing the true lineage diversity in elusive nocturnal organisms is particularly challenging due to their subtle phenotypic variation in diagnostic traits. The cryptic small-eared greater galago (Otolemur garnettii) offers a great opportunity to test if currently recognized subspecies, suggested by discontinuities in coat colour pattern and geographic barriers, represent distinct evolutionary lineages. To answer this question, we conducted the first population-level phylogeographic study of the species, sampling wild specimens from across almost its entire latitudinal range, including the Zanzibar Archipelago. We applied five species-delimitation algorithms to investigate the genetic diversity and distribution pattern of mitochondrial DNA across the geographic range of three out of four subspecies. Our results suggest that far-northern populations of O. g. lasiotis potentially represent an independently evolving lineage, but populations assigned to O. g. garnettii from Zanzibar Island and of O. g panganiensis from mainland Tanzania do not constitute two independent lineages. A dated phylogeny suggests that this northern clade diverged from all remaining samples approximately 4 Mya. Such old divergence age is in line with the split between many galagid species. This northern lineage could potentially represent an incipient species; however, there is not yet enough evidence to support a new taxonomic status for this unique mitochondrial group.

Mitochondrial genetic diversity and divergence dating of Angolan colobus monkeys (Colobus angolensis) in the eastern forests of Kenya and Tanzania: Implications for subspeciation and reconstructing historical biogeography

Whether the Colobus angolensis that reside in the fragmented forests in eastern Kenya and Tanzania represent one subspecies or two has been debated for 50 years. Morphological and more recent genetic and ecological studies suggest that these populations represent two subspecies, C. a. palliatus and C. a. sharpei. However, their distribution of mitochondrial variation remains unresolved since the genetic study only characterized four populations at the range ends. Therefore, we characterized five populations in the area of the hypothesized subspecies divide. We identified eight new haplotypes which, combined with those previously identified, provided 26 haplotypes from nine populations for analysis. Haplotypes found south of the Rufiji River cluster together but separately from northern haplotypes. The largest sequence differences within cytochrome b occur between population pairs representing opposite sides of the river; their mean difference (1.5%) is more than that of other primate subspecies. Analysis of molecular variance attributes most of the variation to that north versus south of the river. These results support the previous subspecies distinction between C. a. palliatus (northern) and C. a. sharpei (southern), divided by the Rufiji River. The estimated time of the most recent common ancestor of all haplotypes indicates that the subspecies have been isolated from each other for approximately 550,000 years. The common ancestor of northern and southern haplogroups was 370,000 and 290,000 years ago, respectively. Nevertheless, the correlation between genetic and geographic distances suggests that isolation-by-distance contributed to population structuring. Significant variation among populations, with only three haplotypes shared between populations, also indicates that an extended period of isolation drove population distinctiveness. Considering these results, we evaluate hypotheses about the founding and differentiation of these subspecies during Pleistocene climatic fluctuations and propose a novel, more direct migration route from Central Africa to their current range navigating Lake Tanganyika, the central Tanzanian corridor, and the Rufiji River.

Biogeographical Importance of the Livingstone Mountains in Southern Tanzania: Comparative Genetic Structure of Small Non-volant Mammals

The Livingstone Mountains (LM; also known as the Kipengere Range) found in south-western Tanzania at the northern end of Lake Nyasa are an important region for understanding the biogeography of Eastern Africa. The two branches of the East African Rift Valley meet here and the mountains might represent stepping stones for colonization and migration between different parts of the Eastern Afromontane Biodiversity Hotspot (especially the link between the Eastern Arc Mountains, EAM, and the Southern Rift Mountains, SRM), as well as an efficient barrier to gene flow for taxa living in drier savannahs in lower elevations. Here we combine new mitochondrial sequence data from 610 recently sampled rodents and shrews with available georeferenced genetic data (3538 specimens) from southern Tanzania, northern Malawi/Zambia and northern Mozambique and compare the spatial genetic structure among different taxa. There is no universal phylogeographic pattern in taxa preferring humid montane habitats. For some of them, the Makambako Gap acts as a barrier between the SRM and the EAM, but other taxa can bridge this gap. Barriers within the EAM (frequently) and within the SRM (sometimes) appear more important. The Rukwa rift between the SRM and the ARM is an important barrier that perhaps can only be crossed by taxa that are not that strictly tied to humid montane environments. For mammals living in lower-elevation savannah-like habitats, the LM can act as a strict barrier to gene flow, and together with the Ufipa Plateau, Lake Nyasa and the EAM create a very similar phylogeographic pattern with three recognizable genetic groups in most savannah-dwellers. The Livingstone Mountains thus appear to be one of the most important biogeographic crossroads in Eastern Africa.

Gene Flow Increases Phylogenetic Structure and Inflates Cryptic Species Estimations: A Case Study on Widespread Philippine Puddle Frogs (Occidozyga laevis)

In cryptic amphibian complexes, there is a growing trend to equate high levels of genetic structure with hidden cryptic species diversity. Typically, phylogenetic structure and distance-based approaches are used to demonstrate the distinctness of clades and justify the recognition of new cryptic species. However, this approach does not account for gene flow, spatial, and environmental processes that can obfuscate phylogenetic inference and bias species delimitation. As a case study, we sequenced genome-wide exons and introns to evince the processes that underlie the diversification of Philippine Puddle Frogs-a group that is widespread, phenotypically conserved, and exhibits high levels of geographically-based genetic structure. We showed that widely adopted tree- and distance-based approaches inferred up to 20 species, compared to genomic analyses that inferred an optimal number of five distinct genetic groups. Using a suite of clustering, admixture, and phylogenetic network analyses, we demonstrate extensive admixture among the five groups and elucidate two specific ways in which gene flow can cause overestimations of species diversity: (1) admixed populations can be inferred as distinct lineages characterized by long branches in phylograms; and (2) admixed lineages can appear to be genetically divergent, even from their parental populations when simple measures of genetic distance are used. We demonstrate that the relationship between mitochondrial and genome-wide nuclear p-distances is decoupled in admixed clades, leading to erroneous estimates of genetic distances and, consequently, species diversity. Additionally, genetic distance was also biased by spatial and environmental processes. Overall, we showed that high levels of genetic diversity in Philippine Puddle Frogs predominantly comprise metapopulation lineages that arose through complex patterns of admixture, isolation-by-distance, and isolation-by-environment as opposed to species divergence. Our findings suggest that speciation may not be the major process underlying the high levels of hidden diversity observed in many taxonomic groups and that widely-adopted tree- and distance-based methods overestimate species diversity in the presence of gene flow.

Redescription of Emplectonema viride - a ubiquitous intertidal hoplonemertean found along the West Coast of North America

Emplectonema viride Stimpson, 1857, a barnacle predator, is one of the most common and conspicuous intertidal nemerteans found along the West Coast of North America from Alaska to California, but it is currently referred to by the wrong name. Briefly described without designation of type material or illustrations, the species was synonymized with the Atlantic look-alike, Emplectonema gracile (Johnston, 1837) by Coe. Here we present morphological and molecular evidence that E. viride is distinct from E. gracile. The two species exhibit differences in color of live specimens and egg size and are clearly differentiated with species delimitation analyses based on sequences of the partial regions of the 16S rRNA and cytochrome c oxidase subunit I genes. In order to improve nomenclatural stability, we re-describe E. viride based on specimens from the southern coast of Oregon and discuss which species should be the type species of the genus. Emplectonema viride was one of the two species originally included in the genus Emplectonema Stimpson, 1857, but subsequent synonymization of E. viride with E. gracile resulted in acceptance of the Atlantic species, E. gracile, as the type species of the genus. We resurrect E. viride Stimpson, 1857 and following Corrêa's designation, this should be the type species of the genus Emplectonema.