Extant species fail to estimate ancestral geographical ranges at older nodes in primate phylogeny

A clade's evolutionary history is shaped, in part, by geographical range expansion, sweepstakes dispersal and local extinction. A rigorous understanding of historical biogeography may therefore yield insights into macroevolutionary dynamics such as adaptive radiation. Modern historical biogeographic analyses typically fit statistical models to molecular phylogenies, but it remains unclear whether extant species provide sufficient signal or if well-sampled phylogenies of extinct and extant taxa are necessary to produce meaningful estimates of past ranges. We investigated the historical biogeography of Primates and their euarchontan relatives using a novel meta-analytical phylogeny of over 900 extant (n= 419) and extinct (n = 483) species spanning their entire evolutionary history. Ancestral range estimates for young nodes were largely congruent with those derived from molecular phylogeny. However, node age exerts a significant effect on ancestral range estimate congruence, and the probability of congruent inference dropped below 0.5 for nodes older than the late Eocene, corresponding to the origins of higher-level clades. Discordance was not observed in analyses of extinct taxa alone. Fossils are essential for robust ancestral range inference and biogeographic analyses of extant clades originating in the deep past should be viewed with scepticism without them.

Identifying structural connectivity priorities in eastern Paraguay's fragmented Atlantic Forest

The Atlantic Forest of eastern Paraguay has experienced extensive recent deforestation. Less than one-third of the region is forested, and the remaining forest largely consists of isolated remnants with potentially disrupted connectivity for forest fauna. We used a graph theory approach to identify those forest remnants that are important in maintaining landscape structural connectivity for mammals in this fragmented forest. We quantified structural connectivity for forest remnants over the period 2000-2019 at three levels: the entire network of Atlantic Forest remnants in eastern Paraguay; at 10 smaller, nested spatial scales (40-10,000 m) encompassing a range of potential mammalian dispersal abilities; and at the level of individual remnants. We used 10 graph theory metrics to assess aspects of network complexity, dispersal-route efficiency, and individual remnant importance in supporting structural connectivity. We identified forest remnants that serve as important structural connectivity roles as stepping stones, hubs, or articulation points and that should be prioritized for connectivity conservation. Structural connectivity was constrained for organisms incapable of travelling at least 9-12 km (farthest distances between nearest-neighboring forest remnants depending on whether smaller remnants were included or not) and was particularly limited for area-sensitive forest-specialist mammals. With the increased forest loss and fragmentation that is occurring, the connectivity of this system will likely be further compromised, but most of the remnants that we identified as playing important roles for structural connectivity were outside of the country's proposed "green corridor," indicating additional areas where conservation action can be directed.

The mid-domain effect and habitat complexity applied to elevational gradients: Moss species richness in a temperate semihumid monsoon climate mountain of China

The utility of elevational gradients as tools to test either ecological hypotheses and delineate elevation-associated environmental factors that explain the species diversity patterns is critical for moss species conservation. We examined the elevational patterns of species richness and evaluated the effects of spatial and environmental factors on moss species predicted a priori by alternative hypotheses, including mid-domain effect (MDE), habitat complexity, energy, and environment proposed to explain the variation of diversity. Last, we assessed the contribution of elevation toward explaining the heterogeneity among sampling sites. We observed the hump-shaped distribution pattern of species richness along elevational gradient. The MDE and the habitat complexity hypothesis were supported with MDE being the primary driver for richness patterns, whereas little support was found for the energy and the environmental factors.

Mitogenomes Reveal Multiple Colonization of Mountains by Rattus in Sundaland

Tropical mountains are cradles of biodiversity and endemism. Sundaland, tropical Southeast Asia, hosts 3 species of Rattus endemic to elevations above 2000 m with an apparent convergence in external morphology: Rattus korinchi and R. hoogerwerfi from Sumatra, and R. baluensis from Borneo. A fourth one, R. tiomanicus, is restricted to lowland elevations across the whole region. The origins of these endemics are little known due to the absence of a robust phylogenetic framework. We use complete mitochondrial genomes from the 3 high altitude Rattus, and several related species to determine their relationships, date divergences, reconstruct their history of colonization, and test for selection on the mitochondrial DNA. We show that mountain colonization happened independently in Borneo (<390 Kya) and Sumatra (~1.38 Mya), likely from lowland lineages. The origin of the Bornean endemic R. baluensis is very recent and its genetic diversity is nested within the diversity of R. tiomanicus. We found weak evidence of positive selection in the high-elevation lineages and attributed the greater nonsynonymous mutations on these branches (specially R. baluensis) to lesser purifying selection having acted on the terminal branches in the phylogeny.

Explaining mammalian abundance and elevational range size with body mass and niche characteristics

Recent work on tropical montane small mammals and birds has shown that abundance–elevational range size relationships (i.e., the relationship between abundance of a species and its elevational range size) can be manifested in a number of distinct generalized patterns. To understand why different patterns occur, one first must understand the causal mechanisms behind patterns of interspecific variation in species abundance and elevational range size. Using small mammal data along five elevational gradients in Southwest China, we assessed the relative importance of body mass, niche position (i.e., how typical the environmental conditions in which a species occurs are of the full set of conditions under consideration) and niche breadth in explaining the interspecific variation in mean abundance of species of small mammals, and elevational range size. Niche position and niche breadth were calculated using outlying mean index analysis based on 24 environmental variables. The relative importance of body mass, niche position, and niche breadth, in explaining the mean abundance and elevational range size of species were examined using phylogenetic regression and phylogenetic path analyses. Along each of five elevational gradients, body mass maintained a nonsignificant (P &gt; 0.05) relationship both with mean abundance and elevational range size when the effects of phylogeny were taken into account. Niche position had a negative effect on mean abundance and elevational range size (species with a niche position close to edge environmental conditions were rarer and had smaller elevational range sizes) across five gradients (significant negative effect: three gradients for mean abundance; five gradients for elevational range size). Conversely, a positive effect of niche breadth on mean abundance and elevational range size was observed consistently, yet the effect was significant only for some gradients (mean abundance: two gradients; elevational range size: four gradients). Our study suggests that niche position and niche breadth both are good predictors of abundance and elevational range size of montane small mammals; niche position and niche breadth therefore play a strong role in the formation of abundance–elevational range size relationship.

Predictive sampling effort and species-area relationship models for estimating richness in fragmented landscapes

Loss of habitat, specifically deforestation, is a major driver of biodiversity loss. Species-area relationship (SAR) models traditionally have been used for estimating species richness, species loss as a function of habitat loss, and extrapolation of richness for given areas. Sampling-species relationships (SSRs) are interrelated yet separate drivers for species richness estimates. Traditionally, however, SAR and SSR models have been used independently and not incorporated into a single approach. We developed and compared predictive models that incorporate sampling effort species-area relationships (SESARS) along the entire Atlantic Forest of South America, and then applied the best-fit model to estimate richness in forest remnants of Interior Atlantic Forest of eastern Paraguay. This framework was applied to non-volant small mammal assemblages that reflect different tolerances to forest loss and fragmentation. In order to account for differences in functionality we estimated small mammal richness of 1) the entire non-volant small mammal assemblage, including introduced species; 2) the native species forest assemblage; and 3) the forest-specialist assemblage, with the latter two assemblages being subsets of the entire assemblage. Finally, we geospatially modeled species richness for each of the three assemblages throughout eastern Paraguay to identify remnants with high species richness. We found that multiple regression power-law interaction-term models that only included area and the interactions of area and sampling as predictors, worked best for predicting species richness for the entire assemblage and the native species forest assemblage, while several traditional SAR models (logistic, power, exponential, and ratio) best described forest-specialist richness. Species richness was significantly different between assemblages. We identified obvious remnants with high species richness in eastern Paraguay, and these remnants often were geographically isolated. We also found relatively high predicted species richness (in relation to the entire range of predicted richness values) in several geographically-isolated, medium-size forest remnants that likely have not been considered as possible priority areas for conservation. These findings highlight the importance of using an empirical dataset, created using sources representing diverse sampling efforts, to develop robust predictive models. This approach is particularly important in geographic locations where field sampling is limited yet the geographic area is experiencing rapid and dramatic land cover changes. When combined, area and sampling are powerful modeling predictors for questions of biogeography, ecology, and conservation, especially when addressing habitat loss and fragmentation.

Endemism and diversity of small mammals along two neighboring Bornean mountains

Mountains offer replicated units with large biotic and abiotic gradients in a reduced spatial scale. This transforms them into well-suited scenarios to evaluate biogeographic theories. Mountain biogeography is a hot topic of research and many theories have been proposed to describe the changes in biodiversity with elevation. Geometric constraints, which predict the highest diversity to occur in mid-elevations, have been a focal part of this discussion. Despite this, there is no general theory to explain these patterns, probably because of the interaction among different predictors with the local effects of historical factors. We characterize the diversity of small non-volant mammals across the elevational gradient on Mount (Mt.) Kinabalu (4,095 m) and Mt. Tambuyukon (2,579 m), two neighboring mountains in Borneo, Malaysia. We documented a decrease in species richness with elevation which deviates from expectations of the geometric constraints and suggests that spatial factors (e.g., larger diversity in larger areas) are important. The lowland small mammal community was replaced in higher elevations (from above ~1,900 m) with montane communities consisting mainly of high elevation Borneo endemics. The positive correlation we find between elevation and endemism is concordant with a hypothesis that predicts higher endemism with topographical isolation. This supports lineage history and geographic history could be important drivers of species diversity in this region.