Genomics and conservation: Guidance from training to analyses and applications.

Environmental change is intensifying the biodiversity crisis and threatening species across the tree of life. Conservation genomics can help inform conservation actions and slow biodiversity loss. However, more training, appropriate use of novel genomic methods and communication with managers are needed. Here, we review practical guidance to improve applied conservation genomics. We share insights aimed at ensuring effectiveness of conservation actions around three themes: (1) improving pedagogy and training in conservation genomics including for online global audiences, (2) conducting rigorous population genomic analyses properly considering theory, marker types and data interpretation and (3) facilitating communication and collaboration between managers and researchers. We aim to update students and professionals and expand their conservation toolkit with genomic principles and recent approaches for conserving and managing biodiversity. The biodiversity crisis is a global problem and, as such, requires international involvement, training, collaboration and frequent reviews of the literature and workshops as we do here.

Speciation rates are unrelated to the formation of population structure in Malagasy gemsnakes.

Speciation rates vary substantially across the tree of life. These rates should be linked to the rate at which population structure forms if a continuum between micro and macroevolutionary patterns exists. Previous studies examining the link between speciation rates and the degree of population formation in clades have been shown to be either correlated or uncorrelated depending on the group, but no study has yet examined the relationship between speciation rates and population structure in a young group that is constrained spatially to a single-island system. We examine this correlation in 109 gemsnakes (Pseudoxyrhophiidae) endemic to Madagascar and originating in the early Miocene, which helps control for extinction variation across time and space. We find no relationship between rates of speciation and the formation rates of population structure over space in 33 species of gemsnakes. Rates of speciation show low variation, yet population structure varies widely across species, indicating that speciation rates and population structure are disconnected. We suspect this is largely due to the persistence of some lineages not susceptible to extinction. Importantly, we discuss how delimiting populations versus species may contribute to problems understanding the continuum between shallow and deep evolutionary processes.

Ecological Divergence and the History of Gene Flow in the Nearctic Milksnakes (Lampropeltis triangulum Complex).

Many phylogeographic studies on species with large ranges have found genetic-geographic structure associated with changes in habitat and physical barriers preventing or reducing gene flow. These interactions with geographic space, contemporary and historical climate, and biogeographic barriers have complex effects on contemporary population genetic structure and processes of speciation. While allopatric speciation at biogeographic barriers is considered the primary mechanism for generating species, more recently it has been shown that parapatric modes of divergence may be equally or even more common. With genomic data and better modeling capabilities, we can more clearly define causes of speciation in relation to biogeography and migration between lineages, the location of hybrid zones with respect to the ecology of parental lineages, and differential introgression of genes between taxa. Here, we examine the origins of three Nearctic milksnakes (Lampropeltis elapsoides, Lampropeltis triangulum and Lampropeltis gentilis) using genome-scale data to better understand species diversification. Results from artificial neural networks show that a mix of a strong biogeographic barrier, environmental changes, and physical space has affected genetic structure in these taxa. These results underscore conspicuous environmental changes that occur as the sister taxa L. triangulum and L. gentilis diverged near the Great Plains into the forested regions of the Eastern Nearctic. This area has been recognized as a region for turnover for many vertebrate species, but as we show here the contemporary boundary does not isolate these sister species. These two species likely formed in the mid-Pleistocene and have remained partially reproductively isolated over much of this time, showing differential introgression of loci. We also demonstrate that when L. triangulum and L. gentilis are each in contact with the much older L. elapsoides, some limited gene flow has occurred. Given the strong agreement between nuclear and mtDNA genomes, along with estimates of ecological niche, we suggest that all three lineages should continue to be recognized as unique species. Furthermore, this work emphasizes the importance of considering complex modes of divergence and differential allelic introgression over a complex landscape when testing mechanisms of speciation. [Cline; delimitation; Eastern Nearctic; Great Plains; hybrids; introgression; speciation.].

Digest: An emerging model system for understanding ecomorphological convergence.

Morales et al. test predictions of adaptive radiation theory and phenotypic convergence in Myotis bats using genomic target capture and a morphological dataset that represents 80% of the species described for this genus. The authors demonstrate that ecomorphological convergence has occurred multiple times throughout the history of Myotis, despite finding no diversification rate shifts associated with phenotypic adaptation. These patterns provide evidence that parallel adaptive radiations can be the result of nonadaptive lineage diversification followed by repetitive exploitation of ecomorphological solutions.

The Origins and Diversification of the Exceptionally Rich Gemsnakes (Colubroidea: Lamprophiidae: Pseudoxyrhophiinae) in Madagascar.

Processes leading to spectacular diversity of both form and species on islands have been well-documented under island biogeography theory, where distance from source and island size are key factors determining immigration and extinction resistance. But far less understood are the processes governing in situ diversification on the world's mega islands, where large and isolated land masses produced morphologically distinct radiations from related taxa on continental regions. Madagascar has long been recognized as a natural laboratory due to its isolation, lack of influence from adjacent continents, and diversification of spectacular vertebrate radiations. However, only a handful of studies have examined rate shifts of in situ diversification for this island. Here, we examine rates of diversification in the Malagasy snakes of the family Pseudoxyrhophiinae (gemsnakes) to understand if rates of speciation were initially high, enhanced by diversification into distinct biomes, and associated with key dentition traits. Using a genomic sequence-capture data set for 366 samples, we determine that all previously described and newly discovered species are delimitable and therefore useful candidates for understanding diversification trajectories through time. Our analysis detected no shifts in diversification rate between clades or changes in biome or dentition type. Remarkably, we demonstrate that rates of diversification of the gemsnake radiation, which originated in Madagascar during the early Miocene, remained steady throughout the Neogene. However, we do detect a significant slowdown in diversification during the Pleistocene. We also comment on the apparent paradox where most living species originated in the Pleistocene, despite diversification rates being substantially higher during the earlier 15 myr.

A species-level phylogeny of Trachylepis (Scincidae: Mabuyinae) provides insight into their reproductive mode evolution.

Trachylepis (Mabuyinae) includes ∼80 species of fully-limbed skinks found primarily in Africa and Madagascar, but a robust species-level phylogeny for this genus is lacking and this impedes studies on a wide-range of topics from biogeography to character evolution. Trachylepis and its close relatives (which together form the Mabuya group or Mabuyinae) are notable in that they have undergone multiple transitions and remarkable specializations in their reproductive modes. A Trachylepis phylogeny will be particularly useful for investigating reproductive evolution, because it includes species that exhibit oviparity, viviparity, and bimodal parity (species with both oviparous and viviparous populations). We sequenced DNA at four mitochondrial and five nuclear loci for 67 (∼84% of) Trachylepis species to infer a phylogeny for this genus. We performed stochastic character mapping of parity mode under a variety of parity mode transition models to infer ancestral parity mode states and the number and type of parity mode transitions. We recovered a strongly supported phylogeny of Trachylepis that is generally consistent with earlier phylogenetic studies. The best-fit model of reproductive mode evolution supports an oviparous ancestor for Trachylepis, and supports at least three viviparity to oviparity transitions. We compared parity mode evolution under the overall best-fit model (no constraints on parity mode transitions) to the best-fit model among the subset of models that assume viviparity to oviparity transitions are impossible. Our results support a model of reproductive evolution that allows for reversibility from viviparity to oviparity, a process that is not generally accepted. Alternatively, the best-fit model of evolution among the set of models that eliminate reversals from viviparity to oviparity suggests that bimodal reproduction may have persisted for millions of years within multiple lineages.

A phylogenetic analysis of the southern African gecko genus Afroedura Loveridge (Squamata: Gekkonidae), with the description of nine new species from Limpopo and Mpumalanga provinces of South Africa.

A molecular phylogeny of the largely rupicolous geckos of the gekkonid genus Afroedura is presented based on a combination of mitochondrial and nuclear gene sequence data. Previously recognized species groups are only partly recovered, with A. pondolia retrieved as very distantly related to the congeners to which it was previously considered allied. Afroedura hawequensis forms a monotypic group that is sister to all other species, which are allocated to the A. nivaria, A. transvaalica, A. africana, A. multiporis, A. marleyi, and A. langi groups. The taxonomic status of species occurring in the former Transvaal province of South Africa (now Limpopo and Mpumalanga provinces) is reviewed based on morphological and molecular evidence. Afroedura rupestris sp. nov. is described in the A. multiporis group, A. maripi sp. nov., A. pongola sp. nov., and A. rondavelica sp. nov., are described in the A. marleyi group, and A. broadleyi sp. nov., A. granitica sp. nov., A. leoloensis sp. nov., A. pienaari sp. nov., and A. waterbergensis sp. nov. are described in the A. langi group. In addition, A. haackei, A. namaquensis, and A. tirasensis, are all raised to specific status. The description of nine new species highlights Limpopo and Mpumalanga provinces as previously unrecognized centers of diversity for the genus Afroedura. A key to the species of Afroedura is provided.