The Importance of Intraspecific Variation for Niche Differentiation and Species Distribution Models: The Ecologically Diverse Frog Pleurodema thaul as Study Case

Climate influences the genetic structure and niche differentiation among populations of the olive field mouse Abrothrix olivacea (Cricetidae: Abrotrichini)

Even when environmental variation over time and space is commonly considered as an important driver of population divergence, few evaluations of intraspecific genetic variation explicitly assess whether observed structure has been caused by or is correlated with landscape heterogeneity. Several phylogeographic studies have characterized the mitochondrial diversity of Abrothrix olivacea, but none has incorporated landscape genetics analyses and ecological niche modeling, leaving a gap in the understanding of the species evolutionary history. Here, these aspects were addressed based on 186 single nucleotide polymorphisms, extracted from sequences of 801 bp of Cytb gene, gathered from 416 individuals collected at 103 localities in Argentina and Chile. Employing multivariate statistical analyses (gPCA, Mantel and Partial Mantel Tests, Procrustes Analysis, and RDA), associations between genetic differences and geographic and climatic distances were evaluated. Presence data was employed to estimate the potential geographic distribution of this species during historical and contemporary climatic scenarios, and to address differences among the climatic niches of their main mitochondrial lineages. The significant influence of landscape features in structuring mitochondrial variability was evidenced at different spatial scales, as well as the role of past climatic dynamics in driving geographic range shifts, mostly associated to Quaternary glaciations. Overall, these results suggest that throughout geographic range gene flow is unevenly influenced by climatic dissimilarity and the geographic distancing, and that studied lineages do not exhibit distributional signals of climatic niche conservatism. Additionally, genetic differentiation occurred by more complex evolutionary processes than mere disruption of gene flow or drift.

How the African house gecko (Hemidactylus mabouia) conquered the world

Alien species are among the greatest threats to biodiversity, but the evolutionary origins of invasiveness remain obscure. We conducted the first range-wide sampling of Hemidactylus mabouia from more than 120 localities across Africa, Madagascar and the Neotropics to understand the evolutionary history of one of the most widely distributed, invasive vertebrates in the world. We used a multi-locus phylogeny, species delimitation, fossil-calibrated timetree, ancestral area reconstruction and species distribution models (SDMs) to determine how many putative species-level lineages are contained within H. mabouia, the timing and tempo of diversification, and the origins of commensality-providing insights into the evolutionary origins of invasiveness. Our analyses suggest 'H. mabouia' originated in the Miocene in the Zambezian biogeographic region and includes as many as 20 putative species-level lineages, of which only Hemidactylus mabouia sensu stricto is invasive and widely distributed, including all Neotropical records. Zambezia is the hotspot for diversity within the group with 14 species in southeastern Zambezia. SDMs suggest that H. mabouia was able to establish in the Neotropics due to habitat suitability, and globalization and the slave trade probably allowed it to cross the Atlantic. Distribution models for the H. mabouia complex overpredict the range of the invasive H. mabouia sensu stricto-highlighting the importance of taxonomy in invasive species management.

Climatic-niche evolution with key morphological innovations across clades within Scutiger boulengeri (Anura: Megophryidae)

The studies of climatic-niche shifts over evolutionary time accompanied by key morphological innovations have attracted the interest of many researchers recently. We applied ecological niche models (ENMs), ordination method (environment principal component analyses; PCA-env), combined phylogenetic comparative methods (PCMs), and phylogenetic generalized least squares (PGLS) regression methods to analyze the realized niche dynamics and correspondingly key morphological innovations across clades within Scutiger boulengeri throughout their distributions in Qinghai-Tibet Plateau (QTP) margins of China. Our results show there are six clades in S. boulengeri and obvious niche divergences caused by niche expansion in three clades. Moreover, in our system, niche expansion is more popular than niche unfilling into novel environmental conditions. Annual mean temperature, annual precipitation, and precipitation of driest month may contribute to such a shift. In addition, we identified several key climatic factors and morphological traits that tend to be associated with niche expansion in S. boulengeri clades correspondingly. We found phenotypic plasticity [i.e., length of lower arm and hand (LAHL), hind-limb length (HLL), and foot length (FL)] and evolutionary changes [i.e., snout-vent length (SVL)] may together contribute to niche expansion toward adapting novel niche, which provides us a potential pattern of how a colonizing toad might seed a novel habitat to begin the process of speciation and finally adaptive radiation. For these reasons, persistent phylogeographic divisions and accompanying divergences in niche occupancy and morphological adaption suggest that for future studies, distinct genetic structure and morphological changes corresponding to each genetic clade should be included in modeling niche evolution dynamics, but not just constructed at the species level.

Genetic Diversity and Demographic History of the Shaggy Soft-Haired Mouse Abrothrix hirta (Cricetidae; Abrotrichini)

Genetic information on species can inform decision making regarding conservation of biodiversity since the response of organisms to changing environments depend, in part, on their genetic makeup. Territories of central-southern Chile and Argentina have undergone a varying degree of impact during the Quaternary, where the response of local fauna and flora was rather species-specific. Here, we focus on the sigmodontine rodent Abrothrix hirta, distributed from 35° S in Chile and Argentina to northern Tierra del Fuego. Based on 119,226 transcriptome-derived SNP loci from 46 individuals of A. hirta, we described the geographic distribution of the genetic diversity of this species using a maximum likelihood tree, principal component and admixture analyses. We also addressed the demographic history of the main intraspecific lineages of A. hirta using GADMA. We found that A. hirta exhibited four allopatric intraspecific lineages. Three main genetic groups were identified by a Principal Component Analysis and by Ancestry analysis. The demographic history of A. hirta was characterized by recent population stability for populations at the northernmost part of the range, while southern populations experienced a recent population expansion.

Species versus within-species niches: a multi-modelling approach to assess range size of a spring-dwelling amphibian

Species Distribution Models (SDMs) can be used to estimate potential geographic ranges and derive indices to assess species conservation status. However, habitat-specialist species require fine-scale range estimates that reflect resource dependency. Furthermore, local adaptation of intraspecific lineages to distinct environmental conditions across ranges have frequently been neglected in SDMs. Here, we propose a multi-stage SDM approach to estimate the distributional range and potential area of occupancy (pAOO) of Neurergus kaiseri, a spring-dwelling amphibian with two climatically-divergent evolutionary lineages. We integrate both broad-scale climatic variables and fine-resolution environmental data to predict the species distribution while examining the performance of lineage-level versus species-level modelling on the estimated pAOO. Predictions of habitat suitability at the landscape scale differed considerably between evolutionary level models. At the landscape scale, spatial predictions derived from lineage-level models showed low overlap and recognised a larger amount of suitable habitats than species-level model. The variable dependency of lineages was different at the landscape scale, but similar at the local scale. Our results highlight the importance of considering fine-scale resolution approaches, as well as intraspecific genetic structure of taxa to estimate pAOO. The flexible procedure presented here can be used as a guideline for estimating pAOO of other similar species.