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opencc-zeroJun 2020View details →

Data from: Cryptic phylogeographic history sheds light on the generation of species diversity in sky-island mountains

Biodiversity hotspots should be given high priority for conservation under the situation of global climate change. The sky islands in southwestern China are characterized by extraordinarily high species diversity and are among one of the world's top biodiversity hotspots. However, neither the actual species diversity in this region or mechanisms generating this diversity are well explored. Here, we report on the phylogeographic analysis of the long-tailed mole (Scaptonyx fusicaudus), a semi-fossorial mammal that inhabits the montane cool forests across the Chinese sky islands and is considered to represent one species divided into two subspecies. Analyses using DNA sequence data from one mitochondrial and six nuclear genes revealed that populations inhabiting different mountains exhibited exceptionally strong geographic structure. The lowlands and large rivers act as "soft" and "hard" barriers to dispersal, respectively, isolating evolutionary lineages for up to 11 million years. Our results suggest that the mountain ranges act as interglacial refugia buffering populations from climate fluctuations, further facilitating allopatric diversification. Strikingly, species delimitation analyses suggests that the long-tailed mole may comprise 18 operational taxonomic units and 17 putative species. Our results suggest that for low-vagility species, the complex topography of the Chinese sky islands has shaped genetic diversity and structure and promoted exceptional diversification through a combination of eco-environmental stability as well as geographic fragmentation. The patterns observed in S. fusicaudus may be representative for other cold-adapted species, reflecting the generation of mammalian faunal diversity in the sky-island mountains of southwestern China.

opencc-zeroAug 2020View details →

Allopatric instead of parapatric divergence in an ectomycorrhizal fungus (Laccaria trichodermophora) in tropical sky-islands

In tropical sky-islands, cold-affinity populations tend to become isolated at highlands during the interglacial periods, and to expand into the lowlands where they become more connected during the glacial periods. Although this has been widely studied in trees, it is poorly understood how fungal symbionts can differentiate among mountains (allopatrically), or within a single mountain (parapatrically) due to climate fluctuations. Here, we conducted population genomic analyses on the ectomycorrhizal fungus Laccaria trichodermophora in three tropical sky-islands using Genotyping by Sequencing (GBS) at low DNA concentrations. There were no significant differences between altitudes within a single mountain, but we observed significant genetic differentiation among populations from different mountains, supporting the allopatric differentiation hypothesis. Our results indicate that L. trichodermophora populations are under a sky-island population dynamics that started during the Pleistocene climate fluctuations.

opencc-zeroOct 2020View details →

Phylogeography and population genetics of pine butterflies: sky islands increase genetic divergence

The sky islands of southeastern Arizona (AZ) mark a major transition zone between tropical and temperate biota and are considered a neglected biodiversity hotspot. Dispersal ability and host plant specificity are thought to impact the history and diversity of insect populations across the sky islands. We aimed to investigate the population structure and phylogeography of two pine-feeding pierid butterflies, the pine white (Neophasia menapia) and the Mexican pine white (N. terlooii), restricted to these "islands" at this transition zone. Given their dependence on pines as the larval hosts, we hypothesized that habitat connectivity affects population structure and is at least in part responsible for their allopatry. We sampled DNA from freshly collected butterflies from 17 sites in the sky islands and adjacent high-elevation habitats and sequenced these samples using ddRADSeq. Up to 15,399 SNPs were discovered and analyzed in population genetic and phylogenetic contexts with Stacks and pyRAD pipelines. Low genetic differentiation in N. menapia suggests that it is panmictic. Conversely, there is strong evidence for population structure within N. terlooii. Each sky island likely contains a population of N. terlooii, and clustering is hierarchical, with populations on proximal mountains being more related to each other. The N. menapia habitat, which is largely contiguous, facilitates panmixia, while the N. terlooii habitat, restricted to the higher elevations on each sky island, creates distinct population structure. Phylogenetic results corroborate those from population genetic analyses. The historical climate-driven fluxes in forest habitat connectivity have implications for understanding the biodiversity of fragmented habitats.

opencc-zeroNov 2020View details →

The fate of páramo plant assemblages in the sky islands of the northern Andes - Appendix S1. Vegetation and occurrence data used in this study

Aims: Assessing climate change impacts on biodiversity is a main scientific challenge, especially in the tropics, therefore, we predicted the future of plant species and communities on the unique páramo sky islands. We implemented the Spatially Explicit Species Assemblage Modelling framework, by i) calculating species' maximum dispersal distance, ii) modelling species distributions at present up to 2100, iii) assembling models into communities. Finally, we assessed the vulnerability of sky islands based on richness and composition changes. Location: Ecuadorian super-páramo (>4200 m) Methods: Using species trait data, the maximum dispersal distance of 435 species was calculated. Species distribution models (SDM) were fitted to obtain current and future distribution predictions based on dispersal and bioclimatic factors. The final assemblages for present and 2100 were achieved by stacking all probabilistic SDMs and applying the probability ranking rule. The vulnerability of each sky island was evaluated by quantifying richness and composition changes. Results: Maximum dispersal distances ranged between 0.008-6027 m/year, and across all scenarios, 70% of models showed a net loss in species distribution while 9% of all species were predicted to undergo extinction by 2100. Local richness was estimated to decrease by 56.63% on average, and composition changes in each sky island suggested a mean loss of 64.74% of their original species pool against a 12.97% gain. Finally, 5% of the sky island floras reconverted from high-elevation to low-elevation species. These numbers were usually more important for high-elevation species and the mountains Pichincha, Ilinizas and Antisana. Conclusions: Our study is methodologically pioneer and provides novel insight on the future of páramo biodiversity. Significant losses in species distribution and changes in community richness and composition suggest drastic impacts and call for further study considering additional factors, such as land-use. Finally, we recommend focusing monitoring and conservation strategies on the northern sky islands in priority.

opencc-zeroDec 2017View details →

Data from: Not seeing the grass for the trees: timber plantations and agriculture shrink tropical montane grassland by two-thirds over four decades in the Palani Hills, a Western Ghats Sky Island

Tropical montane habitats, grasslands, in particular, merit urgent conservation attention owing to the disproportionate levels of endemic biodiversity they harbour, the ecosystem services they provide, and the fact that they are among the most threatened habitats globally. The Shola Sky Islands in the Western Ghats host a matrix of native forest-grassland matrix that has been planted over the last century, with exotic timber plantations. The popular discourse on the landscape change is that mainly forests have been lost to the timber plantations and recent court directives are to restore Shola forest trees. In this study, we examine spatiotemporal patterns of landscape change over the last 40 years in the Palani Hills, a significant part of the montane habitat in the Western Ghats. Using satellite imagery and field surveys, we find that 66% of native grasslands and 31% of native forests have been lost over the last 40 years. Grasslands have gone from being the dominant, most contiguous land cover to one of the rarest and most fragmented. They have been replaced by timber plantations and, to a lesser extent, expanding agriculture. We find that the spatial pattern of grassland loss to plantations differs from the loss to agriculture, likely driven by the invasion of plantation species into grasslands. We identify remnant grasslands that should be prioritised for conservation and make specific recommendations for conservation and restoration of grasslands in light of current management policy in the Palani Hills, which favours large-scale removal of plantations and emphasises the restoration of native forests.

opencc-zeroDec 2014View details →

Data from: Sky island diversification meets the multispecies coalescent – divergence in the spruce-fir moss spider (Microhexura montivaga, Araneae, Mygalomorphae) on the highest peaks of southern Appalachia

Microhexura montivaga is a miniature tarantula-like spider endemic to the highest peaks of the southern Appalachian mountains and is known only from six allopatric, highly disjunct montane populations. Because of severe declines in spruce-fir forest in the late 20th century, M. montivaga was formally listed as a US federally endangered species in 1995. Using DNA sequence data from one mitochondrial and seven nuclear genes, patterns of multigenic genetic divergence were assessed for six montane populations. Independent mitochondrial and nuclear discovery analyses reveal obvious genetic fragmentation both within and among montane populations, with five to seven primary genetic lineages recovered. Multispecies coalescent validation analyses [guide tree and unguided Bayesian Phylogenetics and Phylogeography (BPP), Bayes factor delimitation (BFD)] using nuclear-only data congruently recover six or seven distinct lineages; BFD analyses using combined nuclear plus mitochondrial data favour seven or eight lineages. In stark contrast to this clear genetic fragmentation, a survey of secondary sexual features for available males indicates morphological conservatism across montane populations. While it is certainly possible that morphologically cryptic speciation has occurred in this taxon, this system may alternatively represent a case where extreme population genetic structuring (but not speciation) leads to an oversplitting of lineage diversity by multispecies coalescent methods. Our results have clear conservation implications for this federally endangered taxon and illustrate a methodological issue expected to become more common as genomic-scale data sets are gathered for taxa found in naturally fragmented habitats.

FIGURE 7 in A new species of bunchgrass lizard (Squamata: Phrynosomatidae) from the southern sky islands of the Sierra Madre Occidental, Mexico

FIGURE 7. Habitat at the type locality for Sceloporus aurantius sp. nov., Los Alisos, Sierra del Laurel, Aguascalientes.

FIGURE 3 in A new species of bunchgrass lizard (Squamata: Phrynosomatidae) from the southern sky islands of the Sierra Madre Occidental, Mexico

FIGURE 3. Results of the principal components analyses when all individuals of Sceloporus scalaris group species were analyzed together (a), females only (b), and males only (c).

FIGURE 2 in A new species of bunchgrass lizard (Squamata: Phrynosomatidae) from the southern sky islands of the Sierra Madre Occidental, Mexico

FIGURE 2. Multi-locus species tree from Grummer et al. (2014) derived from coalescent-based analyses of 4,635 base pairs of nuclear DNA. The phylogenetic distinctiveness of Sceloporus aurantius sp. nov. was supported by Bayes factor species delimitation. Numbers at nodes represent Bayesian posterior probability support values.

FIGURE 5 in A new species of bunchgrass lizard (Squamata: Phrynosomatidae) from the southern sky islands of the Sierra Madre Occidental, Mexico

FIGURE 5. Dorsal pattern variation within the paratype series of Sceloporus aurantius sp. nov. from the Sierra del Laurel, Aguascalientes: a) MZFC 25102 (female), b) MZFC 25103 (female), c) MZFC 25106 (male), and d) MZFC 25101 (male).

FIGURE 4 in A new species of bunchgrass lizard (Squamata: Phrynosomatidae) from the southern sky islands of the Sierra Madre Occidental, Mexico

FIGURE 4. Holotype specimen of Sceloporus aurantius sp. nov. (MZFC 28392) in dorsal (a), ventral (b), and in-life (c) views.

FIGURE 1 in A new species of bunchgrass lizard (Squamata: Phrynosomatidae) from the southern sky islands of the Sierra Madre Occidental, Mexico

FIGURE 1. Distribution of bunchgrass lizards in the Sceloporus scalaris group included in this study. Stars denote the known localities of Sceloporus aurantius sp. nov. (yellow star is type locality). Colors of S. brownorum, S. scalaris, S. slevini, and S. unicanthalis match the colors in principal components analyses results presented in Figure 3.

FIGURE 9 in A new species of Lygodactylus (Squamata: Gekkonidae) endemic to Mount Namuli, an isolated ' sky island' of northern Mozambique

FIGURE 9. Habitat surrounding localities where Lygodactylus regulus sP. nov. has been collected: A) Cultivated areas immediately south of Mt. Namuli, with typical native residence; B) View of grassy area above Nanchili Falls, adjacent to the southern face Mt. Namuli. Ukalini forest can be seen in the left background, along with areas being modified for agriculture. C) Same location as in (B) but facing west. Exposed granite rock underneath vegetation is visible in the foreground. The large granite whaleback where paratype PEM R14922 was collected can be seen in the center background. It extends to the right and connects to Mt. Namuli.

FIGURE 8 in A new species of Lygodactylus (Squamata: Gekkonidae) endemic to Mount Namuli, an isolated ' sky island' of northern Mozambique

FIGURE 8. Adult female Lygodactylus regulus sP. nov. in life (paratype PEM R20277, Muretha Plateau, Mt. Namuli; photo: J. Bayliss).

FIGURE 7 in A new species of Lygodactylus (Squamata: Gekkonidae) endemic to Mount Namuli, an isolated ' sky island' of northern Mozambique

FIGURE 7. Adult male Lygodactylus regulus sP. nov. (paratype MVZ 266137): A) lateral view shortly postmortem (grayish blotch extending from right forebody onto dorsum resulted from injection), B) ventral view shortly postmortem, C) dorsal view after preservation, D) ventral view after preservation.

FIGURE 5 in A new species of Lygodactylus (Squamata: Gekkonidae) endemic to Mount Namuli, an isolated ' sky island' of northern Mozambique

FIGURE 5. Yellow ventral surface and black throat stripes of male Lygodactylus rex(top: PEM R16289, Lichenya Hut; bottom: PEM R9778, Lukabula Forest Station).

FIGURE 6 in A new species of Lygodactylus (Squamata: Gekkonidae) endemic to Mount Namuli, an isolated ' sky island' of northern Mozambique

FIGURE 6. Adult male Lygodactylus regulus sP. nov. (holotype MVZ 266138): A) lateral view shortly postmortem (specimen wet from rinse with water), B) dorsal view after preservation, C) ventral view after preservation.

FIGURE 3 in A new species of Lygodactylus (Squamata: Gekkonidae) endemic to Mount Namuli, an isolated ' sky island' of northern Mozambique

FIGURE 3. Ventral scalation of Lygodactylus rex showing enlarged, glandular scales along the ventral surface of the thighs.

FIGURE 2. A in A new species of Lygodactylus (Squamata: Gekkonidae) endemic to Mount Namuli, an isolated ' sky island' of northern Mozambique

FIGURE 2. A majority-rule consensus tree based on Bayesian analysis of the concatenated data set (ND2, RAG-1, MXRA5). Branches with <0.90 posterior probability (PPB) are collapsed, and support values are provided (above: PPB; below: maximum-likelihood bootstrap scores). Branch lengths are proportional to substitutions/site, with scale indicated by the scale bar below.

FIGURE 1 in A new species of Lygodactylus (Squamata: Gekkonidae) endemic to Mount Namuli, an isolated ' sky island' of northern Mozambique

FIGURE 1. Map of selected inselbergs occurring in northern Mozambique and adjacent Malawi. Localities are as follows: 1) Mt. Mulanje, Malawi; 2) Mt. Chiperone; 3) Mt. Mabu; 4) Mt. Namuli; 5) Mt. Inago; 6) Serra Jeci; 7) Serra Mecula Plateau, Niassa Game Reserve. Blue circles mark localities relevant for present study, Mt. Mulanje and Mt. Namuli, and other inselbergs are shaded in green. Red outline demarcates national borders, while white dashed lines demarcate provincial borders.