Article Title: Landscape Genetics in the Subterranean Rodent Ctenomys Chasiquensis Associated

Article title: Landscape genetics in the subterranean rodent Ctenomys “chasiquensis” associated with highly disturbed habitats from the southeastern Pampas region, Argentina. Journal name: GENETICA Author names: Matías S. Mora, Fernando J. Mapelli, Aldana López, María Jimena Gómez Fernández, Patricia M. Mirol, and Marcelo J. Kittlein. Affiliation and e-mail address of the corresponding author: Instituto de Investigaciones Marinas y Costeras, (IIMyC, CONICET), Departamento de Biología, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Argentina. [email protected]

Online Resource 5 Effects of habitat fragmentation and biological attributes on the population structure for several species of subterranean rodents of the genus Ctenomys. All studies have used microsatellite loci, and mostly considered contemporaneous factors as determinants of population structure. Phylogenetic affiliations, common names and literature references are also shown. Suitable habitats for the occurrence of the species were calculated using the package “raster” in R (Hijmans and Etten 2012) with the corresponding georeferenced data of each distribution (this parameter was not estimated in species without accurate information on their distribution)

Species -- common Distribution and extent Landscape Spatial scale Spatial scale of population Most likely determinants of population Reference name -- phylogenetic of suitable habitat configuration among sampling structure structure, patterns of gene flow, and group sites sex-biased dispersal

C. “chasiquensis”. Restricted: limits of the Highly fragmented in Large scale: from Species highly structured at fine Habitat configuration at medium spatial This study. species distribution are not the Eastern edge of 20 to 150 km; over geographic scale. High-medium scale ( 20 km), isolation and habitat Chasicóʼs tuco-tuco, completely known. their distribution. the entire differentiation at only 20 km quality associated to its highly specific Mora et al. Contreras 1968. distributional range among populations. At least 4 environment requirements. 2016 of this species. genetic clusters in the entire study Mendocinus group. area were identified using No isolation by distance at the scale of Bayesian methods. analysis. Gene flow associated to habitat availability (very limited gene flow among sampling sites in the most

1 fragmented environment).

C. porteousi. Highly restricted: less than Highly fragmented. Large scale: from Species extremely structured at Habitat configuration at small spatial Mapelli & about 100 km of linear Farms, forestations, 16 to 90 km; over very fine geographic scale. High scale (10 km), isolation and habitat Kittlein Porteous’s tuco-tuco, extension. degradation of the the entire differentiation among populations quality associated to its highly specific 2009 Thomas 1916 dunes and the distributional range separated by only 10-15 km. Each environment requirements. Suitable habitat for the introduction of exotic of this species. of the eight sampling sites was Mapelli et Mendocinus group. occurrence of their vegetation have been associated with a unique genetic Significant isolation by distance pattern al. 2012a 2 populations: 509 km . highly detrimental in cluster using Bayesian methods. at the scale of analysis, and very limited terms of the viability of gene flow among sampling sites. This this species. species fits to a classic metapopulation system.

C. rionegrensis. Highly restricted: it Highly fragmented in Large scale: from Species extremely structured at Habitat configuration at small spatial Wlasiuk et occupies a small area of 50 the whole species 13 to 64 km; in very fine geographic scale. High scale ( 15 km), isolation, habitat quality al. 2003 Rio Negro tuco-tuco, x 60 km of sandy fields in distribution. nearly the entire differentiation among populations associated to its highly specific Langguth & Abella Uruguay, surrounded by range of this separated by only 15-45 km. Each environment requirements, and the Kittlein & 1970. non optimal habitat for the species. of the eight sampling sites was habitat elevation. Gaggiotti species. There are also associated with a unique genetic 2008 Mendocinus group. three isolated populations cluster using Bayesian methods. No isolation by distance at the scale of in Argentina (restricted to analysis, and very limited gene flow sand dunes). among sampling sites. This species fits to a classic metapopulation system.

2 C. australis. Highly restricted: less than Slightly fragmented Small scale: from Species moderately structured at Habitat configuration at fine spatial scale Zenuto & about 280 km of linear habitat at lower spatial 500 m to 4 km; in a geographic scale. Medium ( 4 km), habitat quality associated to its Busch Southern tuco-tuco, extension along the coastal scales (< 10 km), small portion of the population differentiation at highly specific environment 1998 Rusconi 1934. line of the Buenos Aires considerably species distribution. distances greater than 3 km. At requirements. Province, Argentina. fragmented at larger least 2 genetic clusters in the Mora et al. Mendocinus group. spatial scales (>10 km). entire study area were identified No isolation by distance at the scale of 2006, 2010 Suitable habitat for the using Bayesian methods. analysis. Intermediate values of gene occurrence of their flow among sampling sites. This species populations: 82 km2. fits to a classic metapopulation system.

C. flamarioni. Highly restricted: less than Highly fragmented in Medium scale: from Species moderately structured at Habitat configuration at fine spatial scale Freitas about 500 km of linear most of its coastal 5 to 50 km; in a geographic scale. High-medium (< 5 km) and the environmental 1995 (Flamarion’s tuco-tuco, extension along the coastal extension. Part of its small portion of the population differentiation at instability at larger spatial scales (which Travi 1981. sand-dune grasslands in distribution along the species distribution. distances lower than 5 km. has characterized the environmental Fernández- the state of Rio Grande do coastal sand dunes is conditions of the Coastal Plain during the Stolz et al. Mendocinus group. Sul, Brazil (from Arroio interrupted by Holocene,  50 km) were postulated as 2007 Teixeira City on the north palaeochannels, an important features contributing to the Fernandes to the Chuí River on the urbanizations, lagoons population dynamics and genetics in this et al. 2007 south). Endemic to the first and wetlands, acting as species. line of dunes, associated to isolating mechanisms. the most recent Urban development in Gene flow estimates showed low depositional system in the coastal environments numbers of migrants between the more Coastal Plain. has been highly distant populations ( 40-50 km), and detrimental in terms of higher number of migrants between the Suitable habitat for the the viability of this nearest sampling sites (< 5 km). This occurrence of their species. species fits, most likely, to a classic populations: less than 600 metapopulation system. km2.

C. torquatus. Widespread distribution: It occupies lowlands Medium scale: from Species moderately structured at Gonçalves and Freitas 2009 approach: Freitas occurs in grassland associated to sand 40 to 110 km; in a geographic scale. Population isolation and habitat 1995 Collared tuco-tuco, habitats on the northern fields and gallery minor portion of the configuration as the main determinants Lichtenstein 1830. half of Uruguay and the forests. Despite its entire species Gonçalves and Freitas 2009 of population structure. Significant Gonçalves

3 Torquatus group. southern half of the state wide geographic distribution approach: high genetic isolation by distance pattern at the scale and Freitas of Rio Grande do Sul in distribution, this (Gonçalves and differentiation among populations of analysis. Very limited gene flow 2009 Brazil. species is endangered Freitas 2009). at distances lower than 40 km. among sampling sites at larger scales (> due to the increase of Four population units were 60 km). Higher values of gene flow at Fernandes crop fields and Large scale: from identified based upon 4 sample scales lower than 60 km (Gonçalves and et al. 2009 plantations in central 20 to 400 km; over sites using Bayesian methods. Freitas 2009). Roratto et and southern Rio the entire al. 2015 Grande do Sul. In some distributional range Roratto et al. 2015 approach: high Roratto et al. 2015 approach: Isolation by areas this species is of this species. genetic differentiation among distance was the main factor to structure composed of locally (Roratto et al. populations at distances lower groups of populations. This pattern was large populations. 2015). than 20 km. At least 14 genetic stronger at medium scales (approx. 200 clusters in the entire study area km). Isolation by distance had stronger were identified using Bayesian impact in structuring populations in methods from 21 sampling sites. comparison to the rivers effect as a barrier to gene flow.

C. minutus Restricted: less than about Fragmented in most of Large scale: from Species highly structured at very Habitat configuration at low scale ( 20 Freitas 560 km of linear extension its coastal extension. 10 to 400 km; over fine geographic scale. High km), geographical barriers at larger 2006 Minute tuco-tuco, along the coastal sand- Part of the species the entire population differentiation at scales (e.g. some geographical features Nehring 1887. dune grasslands in the distribution along the distributional range distances lower than 10 km. At like rivers, lagoons, wetlands, and the Marinho States of Rio Grande do coastal sand dunes is of this species. least 12 genetic clusters in the transition between different habitats), and Freitas Torquatus group. Sul and Santa Catarina, interrupted by entire study area were identified and the geological evolution of the 2006 Brazil (from Jaguaruna in palaeochannels, using Bayesian methods. southern Brazilian coastal plain. Isolation Fernandes the North to Lagoa Dos urbanizations, lagoons of populations by distance plays an et al. 2007 Patos at the South). and wetlands, acting as important role in fine-scale genetic isolating mechanisms. differentiation among populations. Also, Lopes it has been postulated a correlation 2011 between natural geographic barriers and chromosomal variations, resulting in a Lopes et al. geographical model of speciation 2013 followed by chromosomal

4 rearrangements.

C. lami. Highly restricted: less than Considerably Large scale: from 1 Species highly structured at very Habitat configuration at lower Freitas about 900 km2, in a small fragmented at the scale to 70 km; over the fine geographic scale. High geographical scales and isolation among 2001 Lami tuco-tuco, Freitas area of 78 x 12 km of of the study. Highly entire distributional population differentiation at populations. High population structure at 2001. sandy fields named modified by human range of this distances lower than 3 km. At small geographical scale, and low levels Fernandes Coxilha das Lombas. actions (this area has species. least 6 genetic clusters in the of gene flow among close populations. et al. 2007 Torquatus group. been intensely entire study area were identified Lopes Suitable habitat for the transformed by the using Bayesian methods. Isolation-by-distance pattern and a clinal 2011 occurrence of their introduction of pastures variation of genetic alleles suggest a populations: less than 600 stepping-stone population model. and non native Lopes and km2. Genetic structure is not associated with vegetation). Freitas distinct karyotypes. This species fits to a 2012 classic Metapopulation system.

C. sociabilis. Highly restricted: endemic Patchy distribution at Very fine scale: High population differentiation at Strongly associated with kin structure Lacey to southwestern Argentina. the entire species locations of burrow very fine spatial scale. among conspecifics (accentuated by sex 2000, 2001 Colonial tuco-tuco, distribution. systems are Differentiation is associated to biased dispersal). Possibly habitat Pearson & Christie, included within an distinct social units. configuration at fine spatial scale. This Lacey and 1985.Not identified. area of 600 x 400 species probably fits to a classic Wieczorek m. Metapopulation system, with high 2004 Not associated to a well- genetic differentiation among social defined phylogenetic units. Environmental instability has group. proposed to explain consecutive historical bottleneck events in population size.

5 The ‘perrensi’ group of Highly restricted: it Highly fragmented in Large scale: from 5 Species highly structured at very Habitat configuration at lower and Giménez et Ctenomys. occupies a small area of the whole species to 400 km; in nearly fine geographic scales. High medium spatial scale ( 10 km), isolation al. 2002 400 x 100 km of sandy distribution. the entire ranges of differentiation at only 5 km and habitat quality associated to its C. roigi: Roig's tuco- fields surrounded by non these species. among populations. highly specific environment Mirol et al. tuco, Contreras 1988. optimal habitat for the requirements. 2010 species in the Corrientes C. perrensi: The Goya Gómez Province, Argentina. Isolation by distance only at smaller tuco-tuco, Thomas 1898. scales of analysis. In general, very Fernández limited gene flow among sampling sites. et al. 2012 C. dorbignyi: This group of species fits to a classic D'Orbigny's tuco-tuco, metapopulation system. Contreras & Contreras 1984.

Torquatus group.

C. talarum. Highly restricted. Continuous habitat Small scale: from Species extremely structured at Mainly habitat configuration at fine Cutrera et Distributed in continental nearly at lower spatial 150 m to 300 m; in very fine geographic scale. High- spatial scale and kin structure among al. 2005 Talas tuco-tuco, Thomas, and coastal sites in several scales (< 1 km), a very small portion medium population differentiation conspecifics (accentuated by sex biased 1898. small populations along slightly fragmented at of the species at lower distances than 300 dispersal). This species probably fits to a Mora et al. the southeastern Atlantic medium spatial scales distribution. meters. classic metapopulation system. 2007, 2013 Talarum group. coast in the Buenos Aires (>1 km), notoriously Parada et Province, Argentina. fragmented at larger al. 2011 Coastal populations scales (> 15 km). present a more continuous distribution than inland populations.